I lay a towel over the sill until I snug the bolts. If I plan on doing a lot of trial and error, I also use fat masking tape along the edges of the door and surround to protect the paint. It's definitely one of the "fiddlier" jobs on the car.
Reminds me of a story...I flew with a guy a couple years ago, and it turned out he was into Mopars. I mean this guy was REALLY into Mopars. With no kids, he had built a world class shop and a real paint booth. He even took in jobs. Not by advertising, but just word of mouth, which means he was good. He said he charges between $25-30k for a paint job, and turns away more jobs than he takes at that price. For the "Bullet" movie 50 year anniversary he put together a Bullet Mustang replica that auctioned for $150k. We are both pretty much self taught, using books and lots of questions at the paint suppliers over many years. The first thing that amazed me is that, when we compared notes...we both used the same paints, supplies, and techniques! I was hoping to pass some good techniques between us, but they were essentially the same...what I have documented in the bodywork thread. What made me think of the story, though, is he was finishing up a pickup truck for his neighbor, and the neighbor wanted to come help with the assembly. Installing the doors and such. He took my number and had me come over to help...as he was scared to death the owner would run a door or hood over another panel and ruin the new paint!! I came over and we put the parts on in a couple hours, before the owner could show up...win win in the end. The finish was preserved and the look of the truck made the owner as happy as if he helped.
The moral is, it's not difficult, but it is a precise job. You must plan the install by laying out your tools and have an idea what order you are going to install bolts and such. Once you pick up the door to fit it, you have already done the install in a dry run in your mind. Having no help makes the planning that much more important. Best of luck!