I started multiboxing with HKN and its great as everyone else has stated, BUT its no longer really supported, information on how todo the more obscure and complex tasks, is hard to come by. If you have programming/scripting experience and you know oops and understand abstraction and your prepared to spend weeks getting HKN to do all the stuff that Isboxer can do then stick with it.
If you want to do that in Isboxer, the wizard will have you running in 5 mins, that was my experience with using Isboxer to create a 5 man team for wow.
I don't think anyone is going to tell you command by command the differences, but the main thing that Isboxer can do that HKN cannot is edit a team in game and apply the changes live using Isboxer that is the IDE (interface development environment) for innerspace (the actual program that does all the smart stuff).
go check the wikki http://isboxer.com/wiki/Main_Page
have a look at MiRai's videos https://www.youtube.com/watch?v=jWYUvNGoEQI
you dont get that with HKN
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