Sounds like you're mounting yours more permanently than I do mine. I tend to move it between our three cars occasionally, so it's pretty temporary and...messy.
I don't even put the antenna on the roof. The MR2's dash vent strip is metal, so it sticks to that. If I use the radio in the Outback, I stick it to the inside of the windshield with a suction cup. If I take it in the SVX, it obviously has to go on the outside of the car, so it goes out the sunroof.