"What would be a less expensive, manual way of isolating one battery? Is that practical?"
The cheapest way would be with a simple battery switch. This link has several examples of battery isolators (diode, switch, solenoid):
http://www.custombatterycables.com/b..._isolators.htm You manually select which battery to use, or you can use both. I've seen these on boats, but they work the same on a vehicle.
It's practical so long as you occasionally switch to the other battery from time-to-time. If you've gone a long time between switching, then I'd recommend you put a trickle charger battery charger on that isolated/hasn't been used for awhile battery to do the charging vice making your alternator do the work.
Some folks don't realize how much strain it places on an alternator to perform the charging of a dead battery. You only want to put your alternator through that when it's your only option.
Now, an isolated battery shouldn't lose too much of a charge, say, over a month or so. If you can remember to flip that switch once a month and drive on the opposite battery for a bit, then you'd be set.
Some folks don't have it in them to remember to do that - some people don't tick that way. So, using a manual switch wouldn't be the best way to go. So long as you're honest with yourself about your ways, then you can figure out what method will work the best for you. If you'll remember it, awesome. If not, another method would be a better option.