Both crew and rooms can be improved with gear, crew can also be trained to improve certain stats. Each one of these alone gives pretty small improvements (like say +1 hp or 0.1 attack), but when combined over 15+ crew and 10+ rooms all those little extras can really add up to make a big difference. Which crew you have and there levels are the most important thing to care about, but once you have good right crew, they can become exceptional when geared and trained properly.
You can equip 1 to 3 Modules per room, depending on your research level and the room size. There are three different types of modules:
Sprinklers are situational (your opponent needs to use Scarlet Missiles or Arson boarders for them to do anything, and you have to have correctly predict the room they'll target). Ignore them.
The other two module types are very useful. Below is a table of what to put in your reactors, shields, teleporter and Android studio. These rooms are all priorities since they'll get focus fired or boarded regularly. Equipping other rooms is nice only if you have spare resources (HA!). Since there are multiple levels of each module, you should complete stage 1 for all rooms, then aim to upgrade everything to stage 2 and so on. It's no good having stage 4 reactor mines if your shields have nothing.
Also remember to stick more than one module in each room where possible (reactors can hold two proximity mines for instance), you'll need the extras to craft the next stage anyway.
Every other powered room (weapons, engines etc) should also use barriesr, however they're much lower priority than SHD, TLP or AS since they're far less commong targets. While you will eventually want a full set of barriers in every room, get your critical rooms setup first, only then exapand to everythign else.
(I didn't list every type of mine/barrier in the game, they're just the easiest to craft/farm. If you want to spend some bux/$$ there are premium options not listed above.)
You can farm these resources needed to craft all these items via the Daily Missions, or buy them off the marketplace.
The Gym lets you train the first 5 stats (HP, ATK, RPR, ABL and STA). At level 5 you can train the other stats (PLT, SCI, ENG, WPN) by building an Academy. Each crew can only be trained a certain number of times, and as you train them it becomes less effective so you need to be careful about who you train in what and when. Training works by increasing stats by a percentage, which means you can make a crews good stats really good, but you cannot make a bad stat good. 50% more of a bad stat is still bad. Training is also quite random. When looking at the options it'll be something like HP ≤ 3%. That means you can expect to gain anywhere from 0 to 3 percent increase each time you train it (the best training offer up to 14%). Sometimes, especially deep into your training you will get 0%, it sucks but it happens.
It gets a little more complicated because you can also research Fitness and Education in the lab to give you more gym and academy training options. Both of these you should be researched when possible. Each level of research gives you more and better training options which lets you specifically target the stats your after. You should always use the best (highest) training available that gives you the stat you want.
Finally there are also training items such as Combat Manuals that you can make or buy. Ignore them for now. Once you get to a level where you need them, you can research it more. I haven't got there yet so I don't use them.
Most training give a percentage upgrade to the current value. This means it's better to train crew in stats that they're ALREADY good in, to make them stellar. On the flip side it's a waste to train crew in weak stats since they won't gain much. In a simple example there is a crew with 10 base HP, you carefully train him to get 50% more HP and now he has 15hp, a gain of +5. However if you do the exact same training on a crew with only 4 HP, 50% extra will only give you 6 which is only a gain of +2. Remember double bad is usually still bad - but double good becomes awesome!
For much more information on the exact mechanics of training checkout the:
But there is one really important question ....
I've put 3 or 4 possible stats below for each role. Pick the best two for your specific crew, a primary and a secondary. You should pick two because diminishing returns means only training one stat all the time becomes useless. Training to many different things just means they're worse at their job (who cares if a boarder has great science?). Training two stats gives a balance between focus and wasteful training. My recommendations are:
Defenders are probably the most versatile in terms of what stats you can train. HP and Ability are the default because usually you want high health and good Crit or Freeze to be good at this role. But if you don't want to train those there are a lot of options including Attack or room stats (e.g. Weapon/Science) for when they're not defending.
Once you know you're stats, find the best training you have for that stat (usually scroll to the bottom of your list in the gym/academy to find the best options you have available). Train in the primary stat first, then secondary. By default train your primary stat untill their training capacity bar is around two thirds full (~60%). Then swap and train the secondary stat for the last 40%. If you want to hit a specific mark (say 100 ability for Rush) training your primary more can do that, but just remember it's really wasteful to go too far into your primary stat so generally you want the 60-40 primary-secondary training split.
There is quite a bit of randomness in training, sometimes you'll strike it lucky and sometimes you won't. Such is the way of Pixel Starships!
If you really screw up there is 1 fix, the Memory Eraser. It will reset all the training for one crew member so you can train them from scratch again. It's expensive and hard to get, so I'd only ever recommend using it on Specials or 7☆ crew, but if you're in a pinch because you trained rush crew in Arrack then this is your fix!
Crew equipment has hundreds of options and combinations and they all have pro's and con's. Unlike modules which are pretty cookie cutter, there is also loads room for personal choice in your gear options. It will also depend heavily on exactly what crew you end up with as they all have different stats, and different slots. Since materials are rare/expensive it's also quite hard to try out loads of different combinations. The stats though for each role stay the same as they do with training. Picking gear is about selecting the right stat for the role, then finding gear that fits in the right slot to buff the stat you're interested in. There are to many combinations of slots and stats to list them all, but here are some examples:
(*For hand +ability I recommend Guitar because it's significantly cheaper, but if you want absolute best then craft Phone instead)
(**For accessory equipment if you can get access to Unknown Material make Mystic Eggs up to Aldara. But since Unknown Material is really hard to come buy with out $$$, go for +weapon as it's the only other option.)
You can farm the resources needed to craft all these items via the Galaxy Map Mining missions, or buy the item or the materials needed to craft it off the marketplace.
Usually sell your materials and just buy the item you want directly ... but it also kind of depends!
You'd think that each item is expensive to buy so it's worth using the materials you get from daily missions to make the items from scratch. That's sometimes true, but it's often more true that the items are cheaper than the materials it takes to make them. Selling any materials you would have used to make it and then buying the item will often end up leaving you with more BUX at the end. This is because Savy often give away complete items and everyone who doesn't need that item sells it driving the price down. The different between what the material crafting cost and the item costs is different per item and changes over time. Here is my calculations from Jan 2020:
Since the change to daily missions when Galaxy update released it's even worse. It's basically never worth crafting now. Sell all your raw materials then buy items directly.
Just don't take on the level 11 when you're level 7 and you'll do just fine. Enjoy!