i just got back from playing five hours of ultimate so I'm really tired.
When I first read the post I was like WTF i do not S D.
Anyhow couple things you can do.
When making cultures dust the flies first and only pour out the first 2/3. use the other 1/3 to feed. that will cut down on transferring mites from one culture to another.
I also use tedion soultion http://www.jtresser.com/drosophila.html
Lastly I keep my cultures in a about 2 inches of water (mites don't swim) I like it way more then mite paper of sprays because you don't have to worry about replacing the paper or how much to apply....
actually another thought. After 4 months move old cultures away form new cultures. Mites are inevitable. but htese steps have worked well for me.