Definitely put the resin down first. Try to make sure that you have pretty even coverage with the resin before laying the cloth on. Once the cloth is down work the resin in to the weave making sure you have full penetration into the glass - then start with your squeegie working the excess resin out. Waves could come from too much or too little resin so a little experimentation on your part is natural. Until you get the hang of it take it slow, one panel at a time. You didn't mention, is this epoxy or polyester resin?

Best of luck,
Dan