Hi rasheika!
I hope your hatch goes well!
I would fill the second reservoir, making sure you have balled up paper towels or a small washcloth of something in there to serve as a wicking agent (if it's just water, it doesn't help the humidity as much; if it's soaked into something else, then it can dissipate more easily). Additionally, if that's still not high enough, stuff little damp paper towels or small washcloths into the spaces between the dividers. Doing both of those tactics, when my house was at 17% in January, I got the humidity to 62% in the incubator.
Yes, you do have to carefully take the eggs out of the trays and lay them on the bottom floor. Make sure you wash your hands carefully before you touch the eggs at this point because they are especially porous!
The cheesecloth sounds cool, but honestly, this incubator is a cinch to clean (especially compared to the styrofoam incubators). I don't know if the cheesecloth could bunch up or not, as one consideration. You don't want it to trap their weak little legs while they're finding their footing. The ducklings did just fine on the floor as it was even before I added the liner I mentioned in the review.
Hope something in there helps! Looking forward to learning from more people!