So, charging two batteries at different times with the same alt is not putting more of a strain on your alt? Dude, if yer alt cant charge one battery, why do you think it could charge two batteries just because it's not doing it at the exact same time? Sounds like you would be in werse shape, you would have two 1/4 charged batteries instead of one 1/2 charged battery. Get a bigger alt and bring your power wiring up to 4awg, the 8 is too small for running two amps. The 4awg will allow the electricity to flow easier causing less amp draw. You might wanna check your alt to be sure its werkin right. I'm running about 800w total and have no problems with a 120amp alt. The main problem seems that the alt is not big enough and your amps are having to pull the needed electricity from the battery. When you drive with your headlights on they probly dim when the bass hits. Check yer alt.
BE SURE YOU FUSE YOUR AMP POWER LEAD AS CLOSE TO THE BATTERY AS POSSIBLE!!!!
Sounds like you may be in danger of melting your amp power wire and causing a fire in your car. Does the 8awg feel hot when your running your system? Bigger wire and bigger alt will solve your problem. Check the wires from the alt to battery also, you want some good 4awg here also, same as your ground. The ground wires, be it for battery or amp, must be at least as big as the power wire. Make sure your grounds are tight and to BARE metal, take some sand paper to the metal if needed.