You're right, the interface could be completely overhauled, and could use some pretty pictures. But the interface is not likely going to be completely overhauled until ISBoxer's replacement, and I don't have an ETA for you on that. My work is cut out for me.
"drag a map key from the main tree to the tree on the left". what the hell does that mean.
Well, sir, the main tree is where you find all of the major pieces of your ISBoxer configuration. It's the top left pane. If you have looked for a single thing in ISBoxer, you would probably understand that as being the main tree. I get that "the tree on the left" is ambiguous and could now be taken as either the top left, or bottom left, but given the context and that there is generally only one, or sometimes two, trees, it is easy to infer the meaning. Because I linked this and because you said you were armed with the documentation, I also have to assume you have seen the following image which is on the User Manual page (which explains the flow of the ISBoxer interface and basic usage of ISBoxer):

The numbers 1 2 and 3 are the order in which you would expect to navigate through the ISBoxer interface.
If you're asking me about "map key" you should note that the term is capitalized and, alone, conveys meaning. It's either a "Mapped Key", or a "Key Map". If you don't know what
these things ARE, then absolutely, refer to the documentation. But, briefly, a Mapped Key is usually a key that is mapped. Like a Hotkey, which would be mapped to do something, like send a key to another window. A "Key Map" is a collection of Mapped Keys.
So yeah.. if you want to get into the meat of using everything ISBoxer has to offer, you're going to need to know how to follow the flow of the interface... and what a Mapped Key is.
Beyond that... well, let me know if you would actually like help with something.