I don’t know what’s going on with your phone! Are you following the eOS installation instructions, step by step?
Anyway, you got it working so hopefully it’s ok.
Backups not so easy, but there are some posts on the forum somewhere about backing up with abdb. I’ve tried it in the past with some success. If I find the post I’ll let you know.
OTA’s are normally OK, but if there is a total mess on the other slot it may cause problems. Next time you do a manual install don’t install the latest rom version, go for the penultimate version. You can then test OTA’s immediately on first boot.
EDIT Here’s the post I was thinking of for backup with scripts and adbd , and the entire thread is a valuable resource too.