I'd recommend you get to grips with Traktor's mapping - it is pretty straightforward once you get the hang of it - find your function (eg select_set_store_hotcue value 1), press learn, then press the iDJ button you want to trigger it. That's it!
(Well, almost - you'll probably want to delete the previous use for that button from the default iDJ mapping.)
I haven't played with iMap properly yet, but if you rely on iMap you won't be able to access any functions not already mapped (like cues) in the default iDJ mapping.
Also, if you use iMap layers, you'll have to remember your iMap layer settings when creating (and using) your Traktor mapping - it is probably simpler to do layers in the Traktor mappings instead so it is all in once place. You can have any number of layers (called Modifiers in Traktor) and you can control them however you wish.
For advanced mapping, check out the recent article on this site that tells you how to make a button store a cue in the next available slot. I'd like to also map a button that selects each cue in turn each time you press it, if I can find a way. That way you could get pretty good cue functionality from a couple buttons. I'll post back if I manage it.
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