2 Apple IDs - 90 day ban?
Currently the 90 day restriction is only for automatic download of additional purchased content.

This also is a per device limitation and not something about the account being banned from working elsewhere. 

For 90 days after you turn on the "automatic download feature", you can't switch another account to start automatic downloads on that one device. You can always trigger updates manually. As long as you disable automatic downloads on the second account (or both) you won't have any issues with your two ID on multiple device setup until you run into the 10 total device limit for a given Apple ID for store purchases.