Good suggestions, guys. I'll sum up:
1) I purchased an SCM module with the RS-2000. Only later did I realize that while it does a number of clever things, battery state of charge monitoring is not one of them. I don't think the Link 10 works with the RS series.
2) I could monitor both the start and the flooded batteries by putting a switch in the sensor wire, as they are both going to be flooded and charged separately from the house bank, which will be 4 8D AGMs treated as one massive 12 VDC battery.
3) The flooded start battery will be fed by the altenator, but could be switched to take charge from the MPPT hooked to the solar/wind if needed, or even a Honda 2000. But as I see myself running the diesel at least once a week, I don't see this as an issue. The flooded windlass battery will be charged by a 20 amp dedicated charger (the current installed WestMarine one, actually) that will be plugged into the house AC as needed, or into the Honda 2000, which, with an output of 8 amps, can charge the windlass battery relatively quickly.
3) The solar/wind will usually charge the AGM bank, but the RS-2000 can do this via shore power, or the alternator output can be switched if needed. I am attempting to minimize the need to run the engine to recharge when on the hook, although I am happy to do so when running under power. Hence the need both for a fairly elaborate set of switches and isolators/combiners, plus the need for accurate state of charge reporting.
4) I've considered that the easy way to do this is simply to hook a voltmeter to the start and/or the windlass battery, and I haven't ruled this out.
5) I will call Ontario Battery. Thanks for the tip. I wonder if they sell Northstar AGMs...my favoured form factor, because I could fit (after some minor bracing and carpentry) four tall, skinny 8Ds under my saloon steps, 12 inches from the Xantrex and less than 36 inches from my alternator...copper the thickness of one's thumb isn't cheap!
6) If this doesn't work, I'll call Xantrex. It's gratifying in a backwards way to find that you more experienced fellows are finding their technical information a little confusing as am I. Thanks!