Delightful. There are several ways to deal with it. I do this:
- For READING mail, my offlineimap knows about multiple accounts and puts them in different directories on disk
- mu indexes the PARENT of all those directories, so as far as mu is concerned, there's a single mail store with ALL the mail. The m: filter can be used to select specific directories, which map to different accounts here
- For SENDING mail, mu4e knows about multiple contexts that are detected based on rules you can set (for instance, when replying to email, it'll set the context to whichever account the mail I'm replying to was sent). Or one can set the context explicitly with the ';' binding.
http://www.djcbsoftware.nl/code/mu/