Hi Geoff,
1)First thing to do is give them a charge while disconected and then take them to an auto shop who can test them with load.
What size outboard you running?
sounds like you are set up with a smaller battery to run electronics when stopped and a larger one for starting.
If you go outside then i would be using the same size larger battery for the backup.
I use 2 100AH batteries (marine) and an auto switch relay /isolator (about $190). Select the battery you wat to run off and it charges both but only runs off the one you select . If it goes flat or fails then you just switch to the second battery and your away.
You don't have to use this but it saves you forgetting to swich between batteries all the time.
In saying this it could just be wiring is the problem. In which case you just need to check all conections.( can take a while)
Hope this is of some help.
Steve.