When I installed my new AC, I bought the plastic condensate drip pan that AS used to use in their AC installations. This is a plastic pan with a curved shape to it that the AC sits in on the roof. The condensate drips into the pan, and the pan accumulates it and funnels it into a nipple that the condensate drip tube is attached to. There is now an alternative available that is essentially two cups that attach under the AC drip points. These cups catch the condensate, and then run it through the double foam gasket that will be under the AC, to meet the condensate drain tube. When you say you have a drain kit what does yours look like?
I also made two wooden inserts that match the curve of the inner skin and outer shell and inserted them between the skin and the shell in the front and back of the mounting hole for the AC. I used hard wood that was about 1.5" wide. This is not there to provide weight bearing support, but to give the mounting bolts something to clamp against, rather than just squeezing the inner skin and outer shell together, and to maintain the curve of the roof. Yes, the metal plate that is used on the inside is still flat, but with the wood supports, it doesn't cause a flat spot in the roof.
My plastic inside ceiling unit does not fit tight against the ceiling, since it is designed to fit agains a flat roof, but the gaps aren't obnoxiously large and don't bother me.