Do not use caulking; use only the specific foam gasket made for your A/C. Also, you should tighten each of the four corner bolts evenly. Count how many turns for each bolt as you remove each one as a guideline to duplicating the original tightness and to keep the A/C level on the roof.
Both Monaco and Lazy Days RV compress the foam gasket to about 1/2 of its original thickness. It's no big deal except that the A/C is heavy and you will have to disconnect some electrical wires to get the gasket in place so mark the wires or, better yet, use a digital camera to take pictures of the wires.