I like to use a sterilite gasket tote for my humidity dome. I put the lid on bamboo twigs so it gets air exchange but keeps the humidity high.
What I currently do is fill the bottom of the tote with water and place solo cups with holes in the bottoms and sides filled with perlite in the tote. Cuttings go directly into the perlite, and the water is wicked up through the perlite so all you have to do is keep the water level from going too low.
Next time I clone I'm going to try a hybrid of my current method and rapid rooters, basically just putting the rooters in the perlite filled solo cups so I get the benefits of both systems.