I formed, poured, screeted and troweled the concrete just like you would a typical sidewalk. We used a mix of one 96 lb sack of Portland Cement to 30 shovelfuls of sand that I mixed in a gas powered mixer (don't use any other aggregate because it would get exposed when you cut the joints). Once the concrete was stiff enough that it wouldn't slump, I drew lines in the concrete in the shape we wanted the stones to be. Then I cut out about a 1 1/2 inch joint all the way through the slab. I would throw the concrete I cut out into the next section we were pouring so I didn't waste it. After the joint was cut, I covered the top of the the individual rocks with crinkled tin foil and tamped it down with a trowel to give the stones some texture. You can stop and start at any section as long as you leave a cut edge where you stop. The next day, I took the flat end of a pick axe and chipped the edges of all the stones to make it look more like flagstone. We colored the concrete with a variety of orange,blue, grey and black concrete stains and very diluted latex paints that we sponged on in random patterns then sealed. Here is a blog post we did while we were working on the courtyard. http://scravings.blogspot.com/2009/06/hard-as-rock-and-warm-fuzzies.html
We originally planted thyme in the joints. It was beautiful when it matured, but became a real weeding headache so we ended up mortaring the joints and adding rocks.

You have done a wonderful job on your landscape. Thank you for the detailed how-to instructions and the blog post with photos. It is a great look that I plan to replicate. (Side note: I also have a son currently serving a mission. I hope all is well in Texas!)