keep them there. I just wasn't sure if it made a 4.4dr1 folder or not, it don't look like it did
If it overwrote your boot5zones, world and stuff, then it went in right. You just need to edit loginserver.ini, db.ini, etc... Also source in that db.sql into your mysql, not sure if much changed from 4.3 to 4.4dr1, but might as well start fresh.