My newest addition, Buddy, has this problem. The fur under and behind his ears is about 4" long and he gets knotted up all the time. Actually, I have to dedicate 10 minutes of brushing once a day or he'll knot up.
The best way to deal with knots is when patience. It's just like untying a knotted shoestring...have the dog lye down on his side and gently work the knot out just a few hairs at a time with a metal comb. It's tedious, arduous work but it will get the job done. After you get the knot out, be sure to brush behind his ears AT LEAST once a day. I tend to run the comb through Buddy's hair anytime I've got a moment.
A tip for removing them...if you're having a lot of trouble, go get some hair conditioner and work some into the matte. This will make it much easier to pull out, but it can be messy. You'll have to dab as you can much of the conditioner out once your done.
Something that can be done as preventative maintancne is to thin the hair out. Go to Wal-Mart (or whatever you have) and find where they keep the hair clippers and stuff for people and buy a small pair of quality thinning scissors...these look like regular scissors but with gaps in the blade. You can use these to thin the hair down on your pooch and it'll make mattes behind his ears much less frequent, and far easier to remove.