Lets review:

You don't want to leave both batteries connected at all times
because A) they are different size & capacity batteries
and B) the charging system is 5 amps and so the starting
battery only gets 2.5 amps and would take a long time to
charge back up. ~ While some here seem to disagree, I've
always heard and it makes sense to me that connecting
dissimmilar batts for a long time ain't that good.

You don't want to replace the 1000 battery, I guess because
that battery *does* make sense for trolling. Plus to do it
really right you'ld need two of the identical battery...something
like two dual-purpose batts. ~ I just bought two dual
purpose for about $110. This actually might be a good
option for you. But read on.

You don't want an A/B/BOTH switch because you seem
afraid that either you or people you lend the boat to
(guests) will accidentially leave it in the Both position. ~
While this makes sense to me....you also have to ask
yourself: How likely is this to happen, for how long, and
what damage will be done. If it's not likely and not a
lot of "damage" then maybe who cares?

Maybe just put a red X on the "both" position. Or, as
Tom suggested, maybe you can disable the both position
in some way.

Also consider your statement: "...I figure I can watch the guage
and just flip the switch when the voltage gets too high..." This
seems to assume you will be watching the gague. It seems to
me that you are more likely to forget to watch the gague
after a while (get distracted by the big fish that's biting) then
to accidentially put a switch into the BOTH position. ~ Same
goes for your guests. If they are smart and ware enough to
remember to flip the switch when the gague does a certain
thing....they are probably smart enought to NOT use the
both position.

You may be suffering from the same thing I often do. I think a
problem through TOO much and want the solution to be TOO
perfect. That's not to say I don't get your points. They seem
all or mostly all valid. And the perfect solution might be out
there. But maybe you need to step back and be simpler about
it.

Good luck,
Gary