Welcome to the forum and I hope you are enjoying your new-to-you bike. They are great touring machines. This forum includes many helpful experts on the care and maintenance of '99 - '09 LTs.
I have an '07 LT and an Aerostich full cover and encountered the same issue on what to do with the antenna when using a bike cover. In order to fit the cover over the antenna, I bought a package of Coghlan's 8 Snap N'Tap Grommets (No. 706) over the internet. After unscrewing and removing the antenna, I put the Aerostich cover on the bike, marking the location where the grommet should go with a felt tip pen. Because the Aerostich cover is very thin and light-weight, I took the cover to a seamstress place and had them sew a reenforcement sheet onto the cover and then they punched the hole and installed the grommet. Using this method, you never need to take the antenna off as the grommet allows you to leave the antenna in place and the blue-colored grommet tells you where the RH rear side of the cover is when installing it. I also never had to worry about the cover tearing after using this method. Hope this helps! :bmw: