I do this as well.
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I didn't pick up ISBoxer until Rift, so it's a bit different there. Basically, I get my alts set up all the same keybinds and then /exportkeybindings <altkeys>, then all I have to do is broadcast "/importkeybindings <altkeys>" and they all instantly configure like I want. Ditto for exporting and then importing the UI settings. Makes cloning configurations a breeze.
As for the ISBoxer config files, considering you can set up a different XML file for each grouping/layout/etc. and have different, specified filenames for each character, it's more or less infinitely configurable. You can aggregate or split things up as much as your methods require.
I actually have 2 wow clients. Makes addons a lot easier.
Curse Client will actually recognize two different clients and will allow you to add addons for each separate client and update them separately, etc. REALLY nice feature.
I have found myself solo queueing tank on my "main" DK, as I'm trying to get him some tank gear to make queueing randoms easier. It's worked out pretty well. I just have to be careful not to move bars around. Obviously with a separate client, there's separate settings involved.
To make a second client all you have to do is duplicate your wow folder(copy paste if duplicate isn't an option). The only pain is that on patch day you have to update both clients. Not a really big deal. I don't fully understand the isboxer config files. I think those are more for the way the isboxer addon works in game. I BELIEVE it has nothing to do with the way other addons work in game.
Keep in mind keybindings and macros will stay the same with 2 clients. I tend to run with less addons when I multibox, and I obviously don't solo play with Jamba. For example I find x-perl easier to set up on my boxed toons, but I prefer ShadowedUF on my solo toons.
All personal preference, thats just the way i run it.
This is good stuff! We all play games for fun! I play wow atm and usually play 5 unless my 'surrogate son' is on then I 'll play four of my toons and round robin them to keep same level. I will solo as needs done for certain things-for example Firelands quests. I have an odd number of 85's so may need to solo for the dailies for that .I use a separate wow install for soloing from my multibox stuff.
I play 5 druid team in dailies. Have a mixed class team I don't play as much recently. Am also leveling a shaman team that are at 75. In these and others I play 17 a day that are alchems, 15 xmute masters. So multiboxing is heavy focus, but I also raid 3 nights a week in top horde guild on server. To my knowledge I'm only player 5boxing on the server, but have met a couple with 2 accts.