Solution for problem one- in order to save manual edits you have to select quit emulationstation from the start menu within emulationstation- if you just shutdown or reboot the whole system those edits are not saved. If you feel this is a big enough issue you can submit it to aloshi at the emulationstation github:

https://github.com/Aloshi/EmulationStation

For issue 2 you submit your report on the same github page.

Controller configuration issues related to retroarch can be submitted to-
https://github.com/libretro/RetroArch

For all of your issues be sure to check the current listed bugs to see if anyone else has posted the same issue. Also be sure to check this forum as some people might have had the same issue as you.

And since you never responded to your previous post indicating people not willing to help from this forum (https://www.petrockblock.com/forums/topic/update-wiki-for-newest-version/) -as promised, instead of a blog I set up a series of videos for setting up retropie 2.6 that might be helpful to you and may answer some other questions you may have.
https://youtube.com/channel/UCYdB7MovoH6yCzkVjTXeiIw also check out floob’s videos as he knows an awful lot more than I do.