Oops, still people out there using BareED?

Anyway, saving the colour scheme (default project) is easy, at least for me, because I am the author of BareED.

Enable "Create Icons?" in the settings menu, in case it isn't checked. Make sure that no characters are in BareED's text buffer.
Customize BareED, i.e. choose the colours, font, screen, window position and so on and save to disk this empty file, say as "Work:Tools/default.def" (as an example). A requester pops up asking whether to create a default project instead of a regular file. Confirm with "Yes".
Now you have two options.
Click double on this created icon ("Work:Tools/default.def") and BareED will be launched with your settings.
The other option is that you manually edit the tooltypes of BareED and enter there "FallbackProject=filename", where you replace "filename" with the path and the name which you chose for the default project ("Work:Tools/default.def" - as an example). Once saved, a double mouse click on BareED's icon will display your settings, the same is valid if you launch BareED by a 3rd party application, f.e. a task bar.
The documentation enclosed to BareED describes it under "Customizing BareED's launch behaviour"; it is the first chapter.
Hope this helps a bit. The other issues you have (1 + 2) I can't comment because I am unfamiliar with those applications.