hooking up 2nd battery to stock stuff?

I'm planning on installing a second battery in my 1992 Camaro. I've done a lot of research but one thing I couldn't find any information on is having the second battery power SOME stock stuff - I've found info on having two batteries powering everything, and info on having the second battery powering aftermarket stuff (amps, etc) but not both. Basically, I'm planning on installing a Yellow Top in the spare tire compartment in the trunk of my car. I got a kit for this from BMR which will make it super easy, and with the AGM battery I won't have to worry about venting or spilling, plus it's a deep-cycle. Rather than installing the batteries with an isolator I got an "Automatic Charging Relay" which connects the batteries in parallel when the alternator is charging, and disconnects the positive cable when it's not, isolating them. I'm going to hook up an amp to the Yellow Top, and a carputer eventually but I would also like the interior lights/trunk lights, headlights, door locks, trunk latch, radio, and power (cigarette) outlets on the Yellow Top battery. What I was thinking of doing is cutting the power to the fuses for the things I want the Yellow Top powering and then running a cable from the Yellow Top to the fuses I disconnected from the hood battery. Is there any reason why I couldn't do this? Anybody done anything like this before or have any tips/advice. I don't want to go into if I should/shouldn't install a second battery, etc. Thanks!

BTW, my main concern is that there are three wires coming from the alternator. There's two in a plastic connector, and one that bolts to the back. I know one goes directly to the battery, but I don't know what the others do. I don't know if the wires going to the fuse box are coming straight from the alternator to the fuse box or if there is something in between (like a voltage regulator?). I also don't know if they are coming off the same cable as that charges the battery, or if they come from one of the different ones that may have different electricity behavior. Essentially the way I'm thinking about hooking stuff up when the car is off the stuff on the Yellow Top would be powered directly from the positive terminal. When the car is running they would be straight from the alternator, from the line that charges the battery.

I understand what you want to do but I do not know why. The easiest thing for you to do is to use two identical batteries in parallel. Sounds like you already have your setup though. You could rewire accessories that you want to run off of the auxillary battery but why?

I never want to worry about not being able to start the car because of a dead battery. Simply having two in parallel would only double the amount of time I can power stuff without the car running. I want it set up so that I can power stuff until the battery dies, and still be able to start the car. The thing I'm hooking up has a switch - when it's off the second battery never gets charged, when it's on the relay closes when the car is running and hooks the batteries up in parallel so they both charge but when the car stops the relay opens and isolates them. I can also turn the witch to manually connect the batteries, so I could essentially jump myself with the turn of a switch. To answer your question about why...right now the only electronics I've added is the alarm. My battery is already well over the recommended CCA for my car, and I just got it tested. Any time I'm working on the car and leave the doors or hood open for more then like 30 minutes, or I listen to the radio or anything it uses enough juice that I can't start the car. I know hooking up a second in parallel would be much easier, but I would rather put in a little more work and have a much better setup. Plus, it isn't going to be that much more complicated really, I just need to know if there's a difference between the cables coming from the alternator because I don't want to hook stuff up to the cable that charges the battery if all the electrical stuff is supposed to be hooked up to the other cable for a specific reason...

Forget the alternator wires. One of them can be used to power an ordinary relay as a battery isolator, but since you already have an isolator.... Rather than reconnect the main cranker, you're probably better using the 2nd battery as a spare, except that that's a yellow top.... So move whatever you want over to the yellow top, but add a low voltage disconnect to protect it. I suggest set for 50% discharge for a deep discharge battery.

So there's no problem connecting stuff straight from the battery to the fuse box? I'll do a search for a low voltage disconnect, I've never heard of one of those. Thanks for the info.

There's no problem provided you aren't mixing the circuits - ie, the new source for the fuse is the 2nd battery; the fuse box "bus-bar" does not cross connect. It also assumes the circuits do not cross power sources down stream and that that could cause problems... Try the MW728 low voltage disconnect - aka "battery protector". It's about $20, handles 10A with cig-socket in & out. If 10A isn't enough, it can turn on a bigger relay instead (eg 400A). It switched on at 12.5V and off at ~11.2V. Non-adjustable, but the 11.2V off voltage can be increased with diodes (0.3-0.6V increments). So too the turn -on voltage, but a manual switch or other relay can short the diodes to get the MW728 to latch on. It does have some delay(s) between on & off (as all "smart isolators" need...), but a "once it turns off it needs a manual reset to turn back on" can also be added.