No you can't transfer incomplete files from one p2p app to another. You can add the complete files for sharing yes. For organising your audio files better, see: Albumwrap/iTunes

Protective software (the 1st 2 have been proven to be the only ones that work properly out of multitudes of duds of that type of program):

ad-ware: http://www.lavasoftusa.com/software/adaware/ (FREE)

Spybot - Search & Destroy: http://www.safer-networking.org/en/mirrors/index.html (FREE)

Peerguardian: http://peerguardian.sourceforge.net/ (FREE)