I like "tacky tape"
http://www.kasonind.com/files/2912/4576/9157/7513-tacky-tape.pngTacky tape, the real stuff actually has the name written inside cardboard tube of tape (see pic in link) I put tape on double thick. I like to trim with plastic putty knife. Then give it couple months, because more tape gets mashed out and tighten screws again if loose and trim again. Then give it a couple months to see if any more putty tape gets mashed out. Then I put on a very thin layer of silicon on top and sides of window just as umbrella for tape. Very thin layer. Be careful with what you clean up old putty tape with (on window frame) I used Coleman fluid, worked really good getting of bits of old tape but also I think it ate the window putty on glass was set in and had to re-do glass seal. When you take out window you might see some plastic or wood spacers. They are for centering window in window frame of RV, Some have spacers and some don't. Before you take out window write down all the little tiny numbers and manufacture just in case you break window. Be on look out for any screws longer then others, if any odd sized make sure to put back into same hole. Don't forget spacers when you put back in. And put any odd ball size screws back into same hole it came out of. If yours has foam tape seal or anything fancy disregard as I have no experience with those. If your window frame has little tiny gap where alum frame comes together (on outside) I covered it up with caulk and got a black felt tip to match color of frame. Clean up of old tape will depend on how old. I was able to do 6 windows in one day on old 5th wheel. And only one window when I had to take back out and was working with newer putty tape. Before I put back in I also turned window upside down and put in bath tub to test for any other water leaks. The vinyl or rubber trim or "ribbon" that covers up looking at inside of window from outside, I picked up new for $2 buck a foot. Most trim shrinks from being exposed to weather.
99% of leaks are the window frame to cut out on rv IMO. When your done should be OK for 10 years or more. Clean your new Lexan with nothing that will show even the littlest scratche. After 3 years every little tiny scratch will show up, so be careful. But stronger then regular glass IMO.