One of the most important concepts to understand in GSB is the balance of weapon penetration and defensive resistance.
It’s often a good idea to have a mixture of weapons with a high shield penetration (such as plasma launchers and some missiles) and armour penetration (such as beams). If you want to destroy enemy ships you will have to have weapons with enough shield penetration to first get through those, so don’t load up on a bunch of beam weapons, which are very cool-looking and deal a ton of damage, but do virtually nothing against shields.
That said, you want to load up your cruisers with at least one reflective shield, which means the difference between certain enemy weapons either bouncing off of them or punching right on through. It doesn’t matter what other shield modules you have - as long as you have one reflective shield, the shields of said ship will have its reflectivity.
Armour is not as effective as shielding for warding off attacks but it is vital for keeping your ships safe from fighters. The more modules you have, the lower the strength of armour (not the hitpoints of it) will be - armour absorbs the same amount of damage regardless of the number of modules, but it can deflect less and less depending on how many modules it must cover. Try to keep your armour strength above the penetration ratings of fighter weapons if you want to keep them from getting swarmed, though the “lucky shot” mechanic ensures that no armour is absolutely impenetrable.
It’s also good to have a general role in mind for what each ship design is doing. I tend to avoid making jack-of-all-trade ships and try instead to make each suit a role depending on its bonuses and other stats - for example, using ships with speed bonuses as fast-strike craft armed with deadly but short-ranged cruiser lasers, or making a carrier that holds anti-fighter weaponry (for warding off enemy fighters chasing yours!).
Those are just a few general pointers, and things I tended to have difficulty with. What sort of problems are you having?