I was going to explain the process, but the article posted by Ken explains it much better than I could have. I have used silicon on saddles that are not too far off, and it worked well. I allowed it to cure fully and trimmed off excess using a soapy water dipped straight-edged razor. Be careful not to cut your covering. If you have a big gap, use the microballoons/epoxy mix. The photos shown in the article show quite a bit more than I would use.

Regarding the unsightly opening behind the landing gear: I would not worry about intrusion of oil etc, but if you can't live with the appearance, build a sturture on the wing bottom to match the fuse lines. You can get some ideas for structure by looking at on-line instruction manuals for Great Planes Extra 300s or you could carve some big chunks of balsa, too.

Like others have said, I would not even worry about trying to lighten up the tail structure, it won't make much difference on this plane. Just don't add weight by adding additional reinforcement structures etc.