Hi, welcome to the forum!
You will certainly have to do a complete sync with MusicBee to your device the first time you do it. Whether there are duplicate files created depends on whether the file naming template you configure in MusicBee matches the currently existing file names. You can set MusicBee not to remove anything from the device, though. For the files that you don't have a copy of elsewhere, why can't you just copy them from the device to your PC?
I believe the MP3 codec is included now, but you can check that by looking in your installation folder for lame.exe in a folder called Codec.