The two batteries in the M550iX are isolated from each other by the Intelligent Battery Sensor. You can safely charge them either individually or simultaneously.
To charge the main battery in the trunk, you can connect directly in the trunk, or use the jump start terminals in the engine compartment to attach clamps, or use a pig tail adapter.
To charge the auxiliary battery in the engine compartment you can connect up directly or use a pig tail adapter.
If you wish to charge both batteries at the same time, AND your battery maintainer is approved to charge multiple batteries, you can do what I did. I installed a pig tail adapter to the aux battery and a pig tail adapter to the jump start terminals in the engine compartment. Then I joined both pig tail adapters with a Battery Minder multiple battery connector:
https://www.batterystuff.com/battery...or-210-ay.html
BatteryMINDer SmarTECHnology® Multiple Battery Connector - 210-AY
I run the Y adapter cable connector out by the passenger (right side) windshield wiper. This way I do not have to constantly open and close the hood to access the battery connectors to charge both. One thing I do, is place a yellow microfiber cloth on the drivers side of the windshield to remind me not to drive off with the charger connected.
Then I charge both batteries with one of two approved battery tenders I own that can charge multiple batteries:
https://www.batterystuff.com/battery...r-128cec2.html
BatteryMINDer 128CEC2 | BatterMINDer 12v 2/4/8 Amp Charger Maintainer Desulfator & Lithium Charger Maintainer
https://www.batterystuff.com/battery...-2365-lcd.html
Battery Saver 6v 12v 50 Watt (4.17A) Maintainer, Pulse Cleaner & Tester - 2365-LCD
Both are approved to charge two batteries at once and I have been doing this for a couple years now without issue. I mostly use the Battery Minder.