Ok, so I went about treating for the flatworms a little differently and thought I would post what I did. Sucking out all those little guys with a siphon seemed like it would it would take forever and I wouldn't be able to get in the rocks, under the rocks etc. I have a lot of rock for a 39g and didn't want to miss a bunch of them.
First, I setup a small tub with 3g of RO and added the flatworm exit to that. Then I setup a larger tub, 5g, with clean saltwater and added the flatworm exit to that. I took out each piece of rock and gave it a bath in the freshwater tub. And I used a turkey baster to blow them off the rock and get into all the little holes. After that, into the saltwater for a while, ended up being close to an hour I think. I left all the rocks with coral attached for last so they didn't get as much time out of the tank.
I added all the rock back to my tank and left it alone for a few hours, mostly because I had to take my dog to the vet. Anyway, after all that, I treated the tank with flatworm exit, used about 1.5 times the recommended dosage. After 5 minutes I could see the remaining worms dying off. After 30 minutes I added my carbon and at the 1 hour mark I did a 25% water change, and siphoned out all the little dead guys I could find.
So far I haven't seen a single worm, but it's only been a day so far. Wish me luck!