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I haven't used Maya with iPi Mocap Studio but as long as the bones/joints names and hierarchy are consistent between the iPi skeleton and your character's skeleton, it should be compatible and you shouldn't have to re-rig. You can do your retargeting in iPi Mocap Studio or you can export the animated rig from iPi Mocap Studio to Maya and be able to retarget the data to your rigged character there. Once you set up a character template, either in Mocap Studio or Maya (or Motion Builder or whatever,) and stick with those conventions, it should work for every mocap motion you create.
If you're new to Mocap, retargeting is either referencing or transferring the data from one skeleton (usually with mocap) to your pre-rigged character. (Actually, there can be lot more going on during retargeting but that's the essential bit.) In other words, you shouldn't need to bind your character to the iPi skeleton, you only need to grab the animation from it and apply it to your own rig. You can create your target rig in any program so long as it follows the usual mocap standards. If you use an auto rigger, it probably has an option for a mocap skeleton with controls on top of the skeleton so you can non-destructively edit the original motion data. The whole point is to rig your character only once and then you can reference the rig that has the mocap (the iPi skeleton in this case) or you transfer/copy the animation from that rig to your own rig. Once you have a standard rig and template, you can pass any new mocap data onto it without re-rigging, and you can have additional controls on that rig so long as it doesn't break the basic hierarchical structure.
Sorry, I can't be more specific than that--it's been a long time since I last used Maya, and I normally work with iPi-Motion Builder-LightWave, but the process is more or less the same for many 3D programs.
Hopefully somebody with more recent Maya experience will pop in and share additional info. :)
G.
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