The update yesterday was reverted, anyone having trouble can just restart their IS and any new problems are gone. I'm correcting those issues before the patch goes live again. The state of IS at the moment is the same as it has been since last August.

As far as the amount of time it takes you to switch, it really depends on how complex your setup currently is, and how closely you want to mirror it. A lot of people are done within a few minutes, between the Quick Setup Wizard and the "Many new Mapped Keys" generator.

As far as switching toons in and out of teams, I do this too. It's perfectly fine to do this, ISBoxer will sync your Jamba team to whatever set of toons you configure. I'm not sure what trouble Mercurio was having, but if you're switching toons on the fly you're going to want to switch it in the Character Set, Export, and either log out to character selection or do a /reloadui. If you don't, then the ISBoxer Addon is still going to have macros active that specify the previous character, and it's still going to insist on putting the previous character in your Jamba team.

Then if you've got a bunch of macros configured in-game specifically for multiboxing, that may or may not get in the way. If you're currently using a focus-based setup, you'll either want to drop that or the FTL. Mercurio for example says he kept his original setup, which since he removed the FTL probably has auto-assist built into the in-game macros (or he'd have to manually assist with an assist key). With ISBoxer, the idea is that you should never have to make macros in-game specifically for multiboxing -- it should be no different in-game than playing solo, except you have several characters. It's much quicker to switch to ISBoxer if you don't have tons of in-game macros specifically for multiboxing.

Anyhow, here's the two guides that you might want for your initial setup (then Ualaa's guide after that when you want more complicated stuff later)
Guide for switching from Keyclone to ISBoxer: http://www.dual-boxing.com/showthread.php?t=30460
ISBoxer's WoW Quick Start Guide: http://isboxer.com/index.php/guides/...de-quick-start