Regarding AquaMail on Marshmallow 6.0, I'd like to help answer any questions you have.
First, let me say I've been running all your latest test versions on our Nexus 6 phones, which are still on stock 5.1.1 and have had no issues. These phones should get OTA updates to Marshmallow 6.0 any day now.
But I've also been running your new releases on my test mule, a Nexus 4 running an AOSP Marshmallow 6.0 ROM. Also has TWRP recovery, Gapps, AFwall+ firewall, SuperSU and all my favorite stuff installed. So it's setup just like for daily use. The Nexus 4 runs this very well.
These phones all have 4 Gmail accounts and 1 IMAP account, provided by GoDaddy, setup in AquaMail.
Anyway, the point of all this is I have the test equipment needed for AquaMail/6.0. I've not noticed any issues with AquaMail on the Nexus 4 and 6.0. But, I don't much care if it goes into Doze mode and doesn't get mail at 2am.
Still, you seem concerned about AquaMail on 6.0. What should I do or look for? I'm not really certain exactly what issues you're worried about.
Android since v1.0. Linux since 2001