I think I may have figured out a fix for the Pebble & Android 6.0 Marshmallow. When Android is updated, by default, it turns on "Battery Optimization" for every app and service except for two, "Google Play services" and in my case, "Motorola Notification".
So if you go into BATTERY> : MENU> BATTERY OPTIMIZATION> and change "NOT OPTIMIZED" to "ALL APPS", you can then select each app or service you want "NOT OPTIMIZED". I turned off a bunch of things including my email app, since I was not getting my emails until I opened the app. (That was the real issue I was searching for BTW.)
I also turned off "BATTERY OPTIMIZATION" for the Pebble App, and it seems to have stopped the disconnects.
My disconnects were also happening from my car to my phone, and I have not noticed that for the last couple of days.
May be worth a shot for anyone with Android 6.0.
( I should also mention, I am still using the app "Bluetooth Auto Connect" and I did turn off battery optimization on that as well.)