T8D electric start unit, problem with alternator

after experiencing problems with my dual batteries (some user error admittedly), I am trying to get to root cause and go forward fix. in the process of making mistakes, i am wondering if I a blew a fuse or some part of the charging process. i had a shop install the unit, and they said that they hooked it up to charge, but i am unable to locate the charging wire set. does it charge through the electric start cables? if not, can anyone provide the wire color coming from wire harness that is the charging wire?

[boats.net]

It charges battery by way of battery cables.

thank you! I am attempting to test the charging capabilty through the battery cables. here is my test procedure: disconnect cables from battery; pull start motor; with motor running, put ohm meter on cables to confirm i am getting 12v dc output. I am getting a nil reading. bad test procedure? likely blown part in motor?