charging batteries

recently replaced my alternator on my 99 chevy prizm with a custom built cnc machined apex alternator due to the stock one failing to charge anything above 12.3/12.5 after replacement it ran did freaking amazing anywhere from 14.9 to 15.2 with headlights and ac on. about 3 days later i was...

Can I charge my secondary battery while my two amps are connected? I always have disconnected both grounds and power wires and take the battery out of my car and charge for a few hours, this process is getting old. I swear people at shows would charge while still connected but I would like to be...