I live in Texas, got an EZ-Pass from NJ when we volunteered with the COE in CT. Never had a problem with getting charged the correct rate for my truck, or when towing my 2 axle trailer. I always do check my statements. (Though we've been out of that area for 17 months).
For the OP - it is ESSENTIAL the extra/ not in use EZ-PASS be wrapped in tinfoil or kept in the static bag. Otherwise both EZ-PASS units will be picked up by the transponders and you will be charged for both EZ-PASS tolls.