I have a customized car with 2 engines. I have no mechanical door opening system for the doors as I have removed it in favor of a remote-controlled electrical solenoid. I have recently installed a capacitive switch to be able to open the doors without the remote. Since I have the switch hooked up to the rear engine battery (that is not the car's primary drive engine), the battery tends to drop over time through non-use. I was wondering if there is a way to hook up some sort of ups system in the car so that the switch will work even if the battery drops too low (this has happened). I have a solar trickle recharger on order to try and help this problem, but I would like a more stable system to be able to open the doors.
You should charge both batteries when either or at least the main engine is running. Add a Schottky diode in series between each battery and the altenator output. If you can, adjust the altenator output up a few 100 mV to compensate for the Schottky diode voltage drop.
Another possibility is to use a relay to short the batteries together once the main engine is running. Deciding "running" isn't as easy as it may sound, but the advantage is that there won't be any voltage drop between the altenator and the charging batteries.
Once both batteries are being regularly charged, you shouldn't need separate power to cover the case when the back battery is dead. Regularly deep-discharging a lead acid battery, especially one intended for a car, is not good. That will ruin its capacity, and make it vulnerable to low temperatures.