Hi @ChaseR,
You’ll need to analyze those separately for most QIIME 2 analyses to make sense. The issue is that you can have V8/V9 reads from the same organism as a V4/V5 read, but (outside of taxonomy assignment, or closed-reference OTU picking which isn’t yet supported in QIIME 2) QIIME wouldn’t know how to relate those sequences to one another. Most of the analyses that you’ll run in QIIME are not dependent on taxonomy (e.g., alpha and beta diversity), so for those analyses a V8/V9 read from the same organism as a V4/V5 read would be treated as observations of different organisms.
We plan to have closed-reference OTU picking supported in the 2017.8 release (due out in late August), so you can alternatively wait for that to process these data together.