Hi @Connor_Geraghty,
First, welcome to the forum!
It think integration of multiple regions is a holy grail in marker gene right now. The only thing I know that - in theory - does this is SMURF. It is umm... there's an implementation ? in Matlab that's basically a series of inhouse scripts strung together and called a day. Pretty dense and hard to use and not QIIME implemented. Ive run their example and it took me maybe... half and hour to profile the sample (with a substantial sacrifice to my swear jar when the FPM reached heights only previously matched when I tried to read SAS.)
But, you may also find this discussion on a similar issue interesting?
Best,
Justine