DarkStar makes a point that is important: Doing a bunch of work on the individual serrations is VERY time consuming. In theory it is the right way to go in order to preserve the shape of the serrations, but getting there requires way too much work for me.
The "flat side first" method is fairly quick and doesn't require much special attention. You *do* need to deburr the serrated side and I always do a little bit of back and forth strokes from the flat side to the serrated side, trying to make sure I reduce and eliminate the burr as much as possible. Just like sharpening a plain blade.
Jason has also pointed out to me in the past that when you sharpen a serrated blade, you have to give in to the idea that you *are* going to change the geometry of the serrations. It's going to happen sooner or later and being hung up on being very exact is just going to prolong it and cost you tons of time. At least that's my take on what he said.
To save time on the serrated side, just continuously push the rod through the serrations, starting at one end and ending up at the other. This is VERY similar to how you use a SharpMaker: Letting the corner of the triangle rod glide through each serration without stopping. Yes, you will glide over the points of the serrations. But trust me, they will remain very very pointy as long as you use light pressure and a fine rod. As I said, I've also used a single SharpMaker rod, set up in the base, to deburr the serrated side, using a "pull down and back" motion. I prefer to do it by hand now, but the SM works well too.
Three years ago I would have told anyone that serrated knives couldn't get impressively sharp, were pretty much all crap, and were a gimmick in the knife world. Now, having owned good serrated blades, and learned the methods to maintain them, I see them as a very interesting and powerful edge type that can get WAY sharper than most people think. I love seeing the looks on people's faces when I show them how sharp my serrated blades are.