If you want to have ProRes under the Custom Quicktime export options, you would need to get the ProRes codec. I think you get it when you buy Compressor and/or FCP. But I would NOT go that way, since exporting to QT ProRes this way (using the QT engine) is guaranteed to give you unintended gamma changes.
The clean way to do it in MC6 Mac (no APR encoding on PC’s thanks to Apple) is transcode or mixdown to APR inside MC, then export Same As Source.
So for instance, if it’s a source clip, just select it in its bin, choose Clip->Consolidate/Transcode, choose Transcode, and select APR. Then export the resulting clip using File->Export->Quicktime->Same As Source.
If it’s a sequence, either transcode the sequence (like you would the source clip), or just mark in and out and choose Special->Video Mixdown, choose APR as the compression type. Dupe the sequence, strip the video, add the mixdown, export same as source.