Here is a simple one I found on the net. Very similar to our applications, just remove the extra fuses etc from the diagram.
http://www.bcae1.com/battiso.htm
Basically, the isolator just goes in-line, between the alternater and the battery.
When I connected mine, I ran new wire from the alternater to the isolator, disconnecting the existing wire that dissapears into the harness. I used a heavy gague wire, like 4 or 6. I took the heavy gauge wire that ran from the alternator directly to the battery (via the wiring harness), and connected that to one terminal on the isolator. I mounted my isolator on the drivers inner fender, right below the battery.
At that point, the charging system should be logically unchanged. All that did was use a different wire to get the voltage from the alternater to the battery. The power is still making it to the battery terminal, so as long as everything is still hooked up, it doesnt affect stuff like the voltage regulator etc.
From there, I ran a length of 4-6ga wire to the back of my van where my deep cycle sits, and connected it to the other terminal on the isolator. Connect a ground lead to the 2nd battery (I ran mine to the frame), and the charging circuit is complete.
My accessories setup is different than yours Im sure, as my van is a camper conversion. Either way, I ran another lead up to a fuse panel, and have all my lights, fridge etc connected to that.
You'll want to seperate your accessories from the main fuse panel, or however they are wired in, so they are getting 12v from the 2nd battery only.
Hope that makes sense.