There are 4 drains. The proper way to clean these is to drop the headliner. Just blowing air through them you can actually blow then off the connector, that would be bad. Two drains at each front door and two in the rear coming out between the bed and cab.
Here is a post I put up on other forum in 2011 after having some major mold issues from my sunroof and third brake light leaking. Anyway, in addition to the sunroof adjustment mentioned earlier, if you have to go the hands on method, this should help you.
Interesting to see a post on this since I unfortunately just had all kinds of water issues which resulted in the carpets having to be replaced. Anyway, I would just like to add some additional info to this, as cleaning the drains is very good advice. There are also drains in the rear. If you look between your bed and rear of the truck cab you will see two little tubes sticking out. These are the exits for the rear drains. If they are clogged the only real way to get at them is to drop the headliner. Not very difficult to do you just have to take some stuff apart. Remove seatbelt bolts, pull out coat hooks, remove grab handles, front and rear, remove front A pillar trim, remove sun visor screws, unplug sun visor, remove sun visor hooks, remove trip computer screw in rear near windshield, pull on both sides of trip computer to release retaining tabs and unplug the molex connectors, remove all of the trim pieces, where the seatbelts were. When all the trim is removed simply pull down the headliner, it is held up by velcro around the sunroof opening. Also disconnect the rear light connector between the coat hooks. You can also disconnect the third brake light connector, I don't think you have though if you just rest the headliner on top of the seats. Also check the third brake light seal for leaks, they are prone to leak. You will now see 4 blue tubes, when the headliner is down, coming out of each corner of the sunroof. Pull the black rubber connector off. If you blow in the tube and hear whistling sound it is clear, if not it needs to be blown out.
When water testing the sunroof (closed) you should only see drips coming out of the drain tubes. If you see alot of water then check the seal. Do this by taking a business card and sliding it between the seal and sheetmetal opening. You should have slight resistance when you remove the card. If there is little or no resistance you need to adjust the sunroof by pulling the accordion black fan look thing (mechanism cover) and then loosen the attaching screws, two on each side. If only one side is bad then adjust that by loosening the two screws and then slide the sun roof forward or back until the seal gives some resistance on the business card.
I learned this the hard way and $600 in new carpet. Hopefully someone else will read this and not have too.
