Car stereos need a contant 12v power supply to retain memory for tuning and audio settings. It will be the yellow wire on the power harness to the back of your head unit.
What gauge wire are you running from the battery to run your Alpine amp? If the amp isn't able to draw enough current to drive your subs, it will not function properly. It could possibly damage your gear. Also check that your battery and alternator are up to the task. Car audio will load up the charging system in a vehicle if it's low powered. You may need to upgrade your alternator and battery.
