For encoding and converting music, I tend to use Media Monkey. The free version can handle ripping to and converting to/from FLAC.
http://www.mediamonkey.com/information/free/
Click on the "Record & Convert" link on the left to see where it mentions that.
Now, I may be misunderstanding what you're trying to do, but I think you may be confused as to how these music formats and their properties work and why your FLAC files generally sound better than your MP3s. Converting your low bitrate MP3s to FLAC or to
a higher bitrate MP3 won't make them sound any better. At best, the result may be a file that sounds just as good as the MP3 you are starting with, but it can never sound better. Your only option would be to re-purchase those songs or re-rip them from your
CDs in FLAC format (or at least in a better quality MP3 format). I believe the CDs will be at 16 bit depth so there would be no use in ripping them to, for instance, 24 bit FLAC.
Encoding audio at low quality in a lossy format like MP3 is like taking a picture of an object through a foggy pane of glass...it's good enough that you can still tell what the object is, but it's not perfectly clear. If you then take a picture of that
picture (ie trying to convert the picture to a higher resolution format), even the best camera will still only be able to give you a really good representation of what the object looks like through the foggy pane of glass. Nothing can accurately derive from
the first picture what the original object looked like without the foggy pane of glass in the way.