If the main power fuse is toast the amp won't come on at all. Simply replace the fuse.. if you had it professionally installed there would have been a large glass fuse or blade fuse in your 330 within 18" of the car's battery. That is the main fuse for everything on that line running from the battery to your amp or amps.
What sub(s) did you have on it and what was the total impedance? JL's will also shut down in certain conditions like a load under 1.5 ohms or when voltage drops below 10V at the amp.
If the amp powers up with 12V applied to it (and a 12v remote turn-on), then it is probably fine and was probably just the main fuse in the 330. Why don't you try powering it up, turning the gains down really low, and just hook up one low level input (rca cable from any source... mp3 player, walkman, portable dvd, whatever) and a sub to ensure that the inputs/preamps are working. Then slowly adjust-up the gains and listen for anything weird. If you have some electrical measurement tools, you can test the output stage easily. With the gains half way up and your source half way up you should read 5 volts on the speaker outputs (or within +-1) If you get a reading in the milivolt range that is a problem.
JL's are rock solid and are very stable at extreme output. The manual is here if you want to refer to some troubleshooting stuff and settings:
http://www.jlaudio.com/amps/pdfs/1000_1_MAN.pdf