Jon,
Yes you can have your ACR and charger too.
Perhaps it is just the drawing, but it looks like you have positive leads going directly to the ground, a practice that is guaranteed not to work.
The instructions for a
Blue Sea ACR show the leads to the ACR going directly to the battery. Running them through switches or busbars can induce voltage drop.
Leading the alternator output directly to the battery or positive bus bar will reduce the chance that someone will kill the alternator diodes by switching the batteries off while the engine is running. Best to run the alternator to the house bank when using an ACR.
I don't understand why the 2 1-2-Both switches are needed. There is a 3 switch solution that uses 2 on/off and 1 dual circuit switch. There have been some recent threads on this.
Can your charger have different charging profiles on each of the output terminals?
Have you checked the fuses on the ACR? A blown fuse(s) will prevent the ACR from working. Is the LED on the ACR flashing? If the Start Isolator is not connected it is possible for the inrush to blow the fuses. Under fusing can also be problematic.
On last thing, thanks for posting your question. It helped me to figure out why my start battery isn't charging, I didn't install the start isolator. One more thing on the To do list.