1) Yes, Jamba should be running as an addon for all your clients. You'll likely want to have the same addons running for each client and have identical setups (at least that's very important to me)

2) No, you only need one copy/install of WoW. ISBoxer will create a new config file for each toon, which saves many of the settings that you'd want.

3.) Don't copy the WoW directory. Use the ISBoxer wizard to set up new toons and new teams (until you know what you're doing, at which time you can do it yourself) and you should be good to go.

Watch the short videos on ISBoxer, they can help. Try to figure some things out as you go - it will help a ton when you run into more complicated issues or want to expand your power through new functionality.