Do people usually send to top 3 programs, or just to their #1? I guess you would word the letter a bit differently for #2 and 3 vs #1. Email or snail mail?
I think e-mail is more convenient. It's the digital age!
You can tell the # 1 program. If you are doing a trio, you can do it various ways... send a gold medal to the top finisher and a bronze metal to the # 3... oh wait... I'm thinking of the Olympics. In reality, you could just tell the # 2 or # 3 that they represent the top 3 on your ROL and that you were impressed with them or you can use the highly popular, noncommittal "ranked highly" phrase.
Some people have faith in the match and do not indicate any preferences... and yet these people still get their # 1 choice. The match really works out if you have faith in it. We are all neurotic, so of course we have to tell # 1 and maybe #2 or # 3 that we liked the program. Honestly, the match process will more than likely match you are one of your choices... unless you're going into dermatology... then it's pure Darwinism. The finch with the largest CV wins.