I have two AGM batteries wired in parallel, they are used to crank the port engine as well as run the house lights etc when the generator is not running. Should I treat and wire install like one battery like ex 10 in the quick start guide sense it’s in parallel or would it be best to wire like step 11 in the quick install guide? 
They are connected together so they are "one battery". even though they have multiple uses. So use step 10, most negative and most positive connections. Make sure all current draws are on the load side of the shunt, even cranking if you really want accurate SOC. Is basically becomes your new negative terminal or connection not the battery.
These shunts are for load on the negative side only. The thin red wire to the positive is for voltage measurement.
If you have another battery bank that shares a negative connection to this bank, you can use a second wire to monitor that voltage through this 712.712 will label the second bank as starter battery.
Also check the cranking current. You don't want to exceed the cabling or shunt rating.
All sources of charge and discharge are conncted to the shunt on the load side. It is marked. Battery positive connections can remain in place.
@kevgermany has some good advice there .
The 712 can monitor either the midpoint of your current bank (setup on step 12) or a second bank as shown in setup 11 in the quick install. (Where your 2x12v is represented by the victron battery)
