No, and no. Are you having problems with the Lil Wil staying on the roof? I've had several Wilson antennas, including that one, and never had a problem before. The only reasons I can think it might come off are: 1- if it's resting on a slightly curved part of the roof, and; 2- there was debris (ice, snow, dirt) between the magnet and the roof (always a good idea to wipe off the magnet anyway, to make sure you aren't about to grind a bunch of metal shavings and other small "shrapnel" into your paint).
As to affecting the propagation, or gain of the antenna, no. The magnet on the antenna isn't designed with anything in mind aside from holding the antenna to the roof (i.e., doesn't affect signal), and a magnet under the roof shouldn't produce any noticeable result at all. There are many more factors on your car (that you can't really control) that might, but that's not one of them.
If you want to increase your signal, upgrading to a Wilson 1000 or 5000 is the best way to do it - the coils larger and made of thicker gauge wire, which helps antenna gain and also makes it more broad-banded (keeps SWR lower across a larger portion of the band). It's all up to how much you want to spend for a slight increase in signal though. Back when we used the radios a lot for the family, and talked from the car back to the base station at the house, I needed to get out 20 miles reliably, and having good antennas (even on stock radios) did the trick. Nowadays, I mostly use mine on the freeway, and I wouldn't pay extra for the slightly better signal. Just my two cents...