Noel Leavitt wrote:

>  I've noticed that while driving, the main battery (the group 41, which
> is brand new) is not charging fully. It's LED remains on yellow most of
> the time.]
> 
>  I am concerned that the real problem is that the two batteries are too
> different in their respective resistance's to charge equally. So the
> greedy deep-cycle battery is hogging all the charge and not leaving any
> for poor Mr. Group 41! 

It _may_ be that the  deep cycle batt would not have been _fully_
charged on purchase, even though terminal voltage would have shown
in excess of 12V.  My own 2x 90Ah deep cycle batteries took approx
20 Amps of charge current between them when initially connected
(initial terminal voltage 13.5 V).  It took several hundred
kilometers of driving (with a 90 Ah alternator) before the charge 
current was down to approx 0.5 Amp (terminal voltage 15 V).   Even 
with moderate (30% discharge) use, initial charge currents can be in 
the region of 25 to 30 Amps.  Don't leave much spare from 65!

The starter battery will probably recover when the deep cycle
battery charges up somewhat - but this will be a recurring problem 
whenever you discharge (i.e. use) the batts.  Get a bigger 
alternator!

>-Do they sell and isolator that provides an appropriate charge to
> each battery

The relative  internal resistance of each batt takes care of that.

>  to prevent the deep-cycle battery from
> sharing in the burden of cranking over the engine, I would find a place
> to connect the relay that only becomes 'hot' after the engine is
> running.

The standard VW/Audi split charge relay (part No.  411915511 B.)
uses the ignition switched live and the blue output wire from the
back of the alternator to control the application of charge current 
to the second battery: ignition 'on' and alternator up to voltage 
allows charge.

HTH
Rich Lumb
'86 Westy