See here:
http://www.xantrex.com/web/id/90/docserve.asp
It is percent charged mode....i.e. 100% then less as you use the batts.
I don't know what you are trying to do from your Honda but the CHARGER portion of your Xantrex puts out 100amps DC or 1200 watts which should be compatible with your Honda unless you are trying to use other stuff at the same time. Are you running your honda through the boats electrical dockside power plug? Do you have any problems with dockside power and your Xantrex or is it just off the Honda that there are issues?
Did you set your Xantrex capacity for about 675 amp hours? I am assuming you have three PAIRS of 6V's wired at 225AH's per pair at 12V. Most Xantrex monitors come preset for just 200ah's.