Well, first don't cover too much as the top is really the only air flow. I doubt a towel will hold in humidity, some plastic (Like a plastic bag) would work. With that set up I would doubt you would have humidity problems since it is set up to hold in humidity. I guess, unless you live in a deep desert. 
Some things to consider: What is your substrate? Make sure when you are misting you are getting it wet to allow it to dry and therefor release humidity slowly back into the enclosure. Paper towels work fine for this if the geckos are small and you don't want them ingesting anything.
Secondly, what are your temps? Too high of a temperature will dry the enclosure much faster than room temp.
Third, make sure you have a water source in the enclosure, a shallow bowl will raise the humidity as it evaporates.
In reality, you shouldn't have to mist more than 2x a day even in dry climates if all things are well. Too much moisture and you encourage mold growth which is also bad. Hope this helps.
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0.1 Albino Leo Gecko
0.1 Crested Gecko
1.0 Dear Boyfriend
Departed: Harvey and Spock