That's potentially a really long answer, unless there's a specific aspect of the process you are interested in? The short version is I've studied comparative anatomy for years (I teach the subject now) including lots of dissections. I also have been able to visit many of the fossil specimens I've restored (and I led a team that mounted about 20 of them in Thermopolis, Wyoming...putting them together in 3D really helped my 2d skeletals).
Having been lucky enough to do those things, even when I'm working from photos and measurements I can generally visualize the bones three dimensionally. For a specific skeletal I generally start by (re)reading all the relevant scientific literature on that species, and often on close relatives (especially if I need to use them to fill in any missing parts).
In terms of the illustration tools I use, I use Photoshop with many dozens of layers, illustrate each bone (I actually wrote a blog post that dealt with some of those challanges recently: www.skeletaldrawing.com/home/t…
). Once they are articulated I illustrate the silhouette on the bottom layer based on the most current analyses of soft-tissue reconstructions (well, the most recent ones I think are correct - like everyone else I have opinions and some of my own ongoing research that influences what I think). Keeping everything on layers like that at very high resolutions means chewing through more RAM, but it also makes it easier to repose and/or update them when necessary.
I generally work on PCs desktops, because I can build my own to save money (especially when shoving 32-64 gb of ram into it). Last year I also started using a Surface Studio, which I've found helps shave a bit of time off the process of illustrating individual bones, which is nice, although I still work in my desktop for scaling, reposing, and often for the silhouette illustration. To facilitate that I've got everything synced through the cloud and I have a fast router and a nice mesh wifi system, so even with GB-sized files I rarely have to wait more than a few moments before I can switch between computers to work on the same file.
I sort of condensed a lot of steps there, but I wasn't sure if you wanted a general overview or were looking for something specific. I hope it helps!