Ignition Wiring Issue, please help.

It's not entirely clear what you have there but I'll take a stab at it.

The fat red wire normally comes from the battery, through a fusible link at the firewall and goes to the ammeter. The fat black wire goes from the other side of the ammeter, feeds most of the fuses and also goes back through the firewall to the output post of the alternator. The ammeter is simply in series with these wires and measures current into or out of the battery. It sounds like they bypassed it entirely which is ok if it's done correctly.

I would check your add-on accessory switch to see if it's properly fused or has a fusible link in series with it. I can't imagine why they would add this unless there was another wiring problem or perhaps they had something hooked up which drew a ton of current. If it were mine I'd get rid of it.