Only issue I could see with running primary in one and emergency drain in the other overflow is water becoming stagnant in emergency's chamber.
Was going to raise the lip height of the overflow with emergency but never did. What I ended up doing was drill a hole in the side of the emergency drain standpipe so I have a small but continuous movement of water. My sump can easily handle the full volume of the chamber in a power outage but I still drilled it up near the top of the standpipe and have a 1/4"OD tubing running to the bottom. Since hole is near top, that's my siphon break.
I'm also running a 20g fuge separate from my sump and just tee's the primary drain. About 200gph to the fuge rest to the sump.
Here's my post on converting from dual Dursos to the Herbie.