Hmm, Chuchu, I think your issue is simply one of a bad powerplant. Just buy one of those "confusing" powerplants, which boast improved thrust recharge rate (helps with thruster regeneration).
The relationship between thrusters, engines, and weapons is pretty much this: the yellow energy bar at the bottom of the HUD (your reactor capacity) denotes the power available to all of your ship's systems.
- When you fire a weapon, it pulls the energy from this reactor, causing hte energy level to dip for a second before it is regenerated. Pretty straightfoward.
- When your are moving under power of your engines, you are using that yellow energy. Most engines do not drain the powerplant while flying at regular sublight and dogfight speeds, but once Cruise is engaged, some engines cause some reactors (notice I didn't say ALL reactors) to drain. This is simply part of the balance, i guess - if your ships was hurtling at over half a kilometer per second, I'm betting that it'd take a little extra enregy than normal, no?
As a side note, a lot of people don't realize this, but if your ship is having trouble with weaopn energy, try killing your engine when in combat: use your thruster in quick and careful bursts to redirect yourself, but leave your engines off. This will eliminate a small (but still important and influential)amount of power drain, letting you fire for a few more seconds as well as helping your recharge rate
- When you use your thruster, the ship takes energy from the power plant to regenerate that power.
In all cases, the basics of combat use a little energy, which has to come from somewhere
But do try other powerplants ... and a better ship wouldn't hurt
*there are other better ships out there, thrust me*
Anyways, hope this helped your question.
"Do or do not. There is no try."
- Jedi Master Yoda