I don't understand the question.
Are you creating these separate file types to sync to your devices and then seeing them hang around unwanted in your library, or do you have these multiple versions on purpose to begin with only want a certain format to reside in your library?
If it's the latter, I keep my FLAC files in a separate directory from the files I import into my music library. That's the most simple answer.
You can also select only certain types of files to import by going to File->Scan Folders for New Files, checking "Restrict scanned file types," and selecting which types you'd like to restrict.
I'm not sure how importing works or if it even happens in the former case because I don't transcode on the fly, but I don't think files transcoded on the fly get automatically added to your library so if that's what's happening something is likely going wrong there.