I'm also a big fan of the truckers hitch for a perimeter line. I use a small loop of a figure 8 to pull the rope through and back on itself. The truckers hitch allows you to adjust tension on the rope easily.
I run the rope in a continuous loop through all D rings, but I don't like to tie the line to any D rings. I do this for a couple of reasons. If anyone is entanged in the perimeter line I want to be able to cut it from anywhere to free them and not have to hunt down a section between two knots. Also when rope is tied to the end D ring as the raft is deflated and re inflated it puts more tension on one side of the D ring leading to the D ring enventually failing. Different strokes for different folks.