There have been several discussions about the ship having limited power (which I myself think is a brilliant idea), so you might not be able to do multiple things at the same time. One thing that might make preforming power-hungry tasks easier is the capacitor bank. Basically, it allows you to slowly charge up a large bank of electrolytic capacitors at the cost of a bit of power from your ship (probably even after it's full from charging, because of leakage). You can then release the capacitor bank's power over a time determined by how much power is being drained.
The capacitor would be a 1-meter-sized-cube with an integrated controller. The cube would have a control panel that would allow setting the charge limit (you could keep it from sucking up all of your power), the discharge limit (so it doesn't dump all of its power into a fragile component all at once), and a physical disconnect (which physically internally disconnects the capacitor bank from the control circuity to slow leakage; dis- and re-connecting should take a while, say 5 seconds).
The applications of this are vast. For example, a small scout ship might only generate enough power to have lights, run the engines at 50%, barely keep the shield up, and run the the CPU at 400 Hertz, with maybe 5 W/s (watts per second) left. 5 W/s isn't much, but you could slowly charge the cap bank up with that surplus power, then use that power to run the engines at a higher speed, use a short-distance warp engine, or raise the shields.
Another application might be to give the CPU its own capacitor bank and have it run at about 100Hz (that's orders of magnitude slow). When you have to do something that'll take a long time, like floating-point math, (heaven forbid) a bubble sort, or (HEAVEN FORBID) a bogosort (just kidding
), the CPU tells the capacitor to release its power fast enough so it can run at 100kHz while it does that operation.
EDIT: I forgot to mention, everything controllable by the cap bank's control panel should also be controllable through the CPU.