It works the same as always.. You'll have to elaborate on the "can't seem to change" part. As in setting the background is not doing anything? Are you actually hitting Save in the settings window? Or did you even find where the option is to set it?
Also if you're trying to quickly color match for atlasing, you can also Alt-Click anywhere on the model and this will temporarily set the color of the background. It is only for that window though and doesn't persist, so if you need a specific color it's best to use the Settings window still.
For Skyrim definitely just use the latest... For Morrowind there's always the possibility that I've dropped the ball on support for it somewhere, either nif.xml compatibility or something in the actual program. Just use the latest until you run into issues, and please report said issues as obviously lapse of support for any NIF version is not intended.