It is always best to read and follow the manufacturer’s documentation. The manufacturer envisions, designs, validates, tests then documents the correct method to properly implement the equipment. That is always superior to blundering along w/ the seat-of-the-pants “act first then think” method.
The wiring and installation should always meet or exceed all ABYC standards.
The Blue Seas SI-ACR P/N 7610 is part of the Blue Seas 120A Add-A-Battery Kit.
The installation diagram does not depict the battery charger wiring, but that should be a dual bank charger, wired to each battery bank, per ABYC.
WRT to mixing battery chemistry, using an AGM and a flooded cell, that is not advised. That combination will function, but the dual-bank charger can select only one chemistry, so one bank will be charged per the recommended profile and one won’t. Also, when the ACR is routing power, one battery will be working harder.
The most important part is that the AGM wants lots of charging current and the flooded cell doesn’t. As such, the charging current output for the Dual Pro charger is too low for the AGM battery.
This reply has links to manufacturer’s information on AGM and flooded-cell batteries and charging. This [rul=http://www.thehulltruth.com/4993905-post7.html]reply shows that AGM wants at least 0.2C charging rate and flooded cell wants c/10 rate.
Wire the ACR to the key switch per the instructions.