The fact you have a second 'lesiure' battery connected is not important to a lot of the BMVs info, especially the Voltage. It is not different to the Starter Battery and Alternator being there - when your charge relay is on, you have THREE batteries in place, only one which is "known" by the BMV. the other two are just 12V load/supplies.
You just need to be aware that the SOC calulation and Ahs used from the BMC data is only for the main battery and not the entire system, so is not giving you the full picture.