Help needed please!

Okay i have installed amp and followed everyones instructions and advice.
Front and sub amped, power one way, speakers etc the other.
Was all finished so i started testing, was sounding good and booming BUT then all the power went, stereo went off, tried car, wouldnt start.
Checked all fuses, none blown. Checked battery and its flat.
Have put battery to charge overnight.

Has this happened because i was testing without the car running and ive just drained the battery (i was powering it hard but not for anymore than half hour) or is this gonna be a bigger problem do you think?
Should you always have the car running when booming the stereo??

Any help real appreciated guys and gals!