[Suicide Junkie]

Run out and not be able to get any more?

Are you by any chance using a High Energy Discharge weapon on a ship without a quantum reactor or three?
The Wave Motion Gun may be superpowered, but it sucks down a ton of energy for at least 30 seconds when recharging.

If you stick with conventional weapons like torpedoes and bolts, you should have no problems on a ship with a small storage tank and a couple double reactors.
Heck, if you carry a pair of big energy tanks, you can fight almost anything without any reactors at all.
The trick, of course, is to not go around always firing. You've gotta let your batteries charge up and your guns cool down every now and then. Having lots of reactors is not a bad thing... they're cheap and small, and there is no limit to the number you install.