Maybe TMI, But I'm Concerned

Vincent got sent home from school with a fever and vomiting last Wednesday. He's had a fever kind of on and off and has been complaining of ear pain (in varying degrees) since then. I've always heard lots of times ear infections will just work themselves out, and that a lot of times antibiotics aren't the solution. I held off taking him to the doctor until today, due to a majorly bad day yesterday. He really went downhill, so I kept him home from school today, too. We went to the MedPoint clinic and saw the nurse practitioner. He's been mostly complianing of pain in his left ear, and hasn't really even mentioned his right at all this whole time. The NP told me his right ear drum was red and inflamed but said she couldn't really even see the left due to the wax that was in his ear.

Nonetheless she prescribed some analgesic drops and Amoxicillin. Oh yeah, he's been saying he was dizzy, too. I put the drops in his ears twice today and he's now had two doses of the antibiotics. He has pretty much stopped complaining of the pain, and looks to be feeling better than he did yesterday. My question is this...

After I put the drops in the 2nd time, I put clean cotton in his ear to keep it from leaking out. Tonight, when I was getting him ready for bed, I noticed the cotton ball was really wet. I took it out and saw A LOT of crud inside his ear. It didn't stink or anything, but I got a bunch of watery stuff, pasty whitish stuff, and what looked like small wax fragments out with some Q-tips. While I was pulling his ear back to clean and while I was using the Q-tips, I could actually hear his ear popping from where I was sitting. It sounded just like it does when my own ear pops, but it was his and I could hear it. Also, he said there were funny noises in his ear (whistling that he said sounded like music) earlier after I did the drops. I'm concerned that his ear drum has ruptured. If so, what would I expect to see as far as drainage? Why did I hear the popping? Has anyone had any experience with this kind of thing? The web says that "minor" perforations heal on their own... any one out there ever had a kid with a perforated ear drum from an infection? If his ear drum actually perforated because of an inner ear infection, wouldn't you think the "crud" would be stinky, or otherwise more remarkable than it was?