How do you count weight (boots and clothing)?

The answer depends on you. These measurements are only useful for three things: quantifying pain, trip planning, and analyzing your current setup with an eye to going lighter. Beyond that, once you set foot on the trail, your load weighs whatever it weighs.

I know some folks who only think in terms of FSO (From Skin Out) weight, since it tells them how much everything weighs. I've noticed that many of these folks use their clothing pockets to store parts of their kit in: pocketknives, compasses, snacks, etc. So, for them, the FSO probably provides the most accurate measurement.

I don't do that - everything is somewhere in my pack (gotta love hipbelt pockets!) Since I wear clothes everyday, and am used to carrying the weight of my clothing around, I don't find it useful to add that in. So, I only count the weight of my pack and everything in it. When I'm planning, I usually include a liter of water and food for however many days I'll be out. But the only purpose in doing so is to analyze whether there's anything I can safely and comfortably leave out to lighten the pack (more and more often, there isn't.) It also lets me play with how much "luxury" I can afford (for example, in the summer I almost always take a chair kit; in winter, when I'm carrying extra clothing, I often leave it behind, since the days are shorter and I won't be sitting around in the evening.)

I tend to aim for a target weight of 25 pounds at the trailhead; that seems to be comfortable to carry for me. How did I arrive at that? My ideal weight is about 190 pounds; 20% of that is 39 pounds for a maximum comfortable load - one I could carry 8 - 10 hours without being totally exhausted, staggering down the trail. I'm about 10 pounds above my ideal weight, so I subtract that from my maximum load - carrying overweight poundage is no different from carrying gear - which gives me a max load of 29 pounds, which I round down to 25 as a goal. The 20% is a general rule of thumb; some people say 15%, some say 25%, and I even know trail animals who use 33% as their target. 20% seems to be a good number for me, based on my own experience over the years.

Consistency and usefulness are the criteria for how you choose to measure your pack weight. Find the system that is most useful for planning purposes, and stick with that.