Win 10. Also can you tell me what the base directory should be in settings? For some reason files are not saving in the correct overwrite files and things aren't updating like they should.
Not sure what you mean by the bolded phrase.
The rule of thumb in MO/MO2 is this: If the file exists in the VFS it is updated, if it is a new file it will go to 'Overwrite'.
It is best practice to keep 'Overwrite' clear by either creating a new mod from its contents or by dragging the contents into the correct mod.
The only time this rule changes is with an odd behaviour when using xEdit and cleaning/editing some plugins. This is believed to be related to drive speed and OS file permissions not releasing in time before the process has completed.