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not sure i'd put the towel over them, first because evaporating water lowers temperature immediately near it, and also, i want max air circulation aorund the eggs, and wet paper towel (even dry) will decrease the air flow.
what I do is layer the paper towel on the wire, under the eggs, and put the eggs on a paper towel lined cookie tray (the kind oreos come in). then if i need to dampen the paper towel on the bottom the eggs stay dry. the paper towel on the cookie tray is just to give traction. the bare plastic is slick. an added benefit, the rows on the cookie tray keep eggs from shifting much when hatched chicks decide to go wandering.
and with the paper towel on the bottom (make sure you don't cover the air holes at the edges), i fill all the water compartments in the tray underneath, and enough moisture makes it up thru to keep the humidity about 55-60 and when i have external pip I pour a small bit of HOT water onto the paper towel to crank it up a bit more short term.
I'm also bad about continually openning the hatcher to check progresses, so when i do i add a bit more hot water to the paper and it's back up over 70% within a minute. once the paper on the bottom dries out it goes back to where it was before.
this is a pic i posted before but it shows the cookie tray idea...