Hello Brittany,
Do the separate regions have separate barcodes, so that you can easily split them? If so, I would split them and treat them like two different data sets and never process them together ever, just like if you had sequenced 16S and ITS regions.
Dealing with multiple regions is a big challenge, but the good news is that we great thread going discussing all parts of the problem. But hopefully you can separate your regions and avoid this messiness.
Colin