How is this properly done, specifically around a tree or boulder? Are there do's and don'ts from an efficiency stand point? Are there do's and don'ts from a safety stand point? If you intend to lead the next pitch too is it better just to use a cord?
Your question is quite broad with many possible answers. I agree with LL on everything he said (hell just froze over), but I'll add some thoughts on some situation specifics;
1) If you are leading the next pitch I don't think using the rope is the way to go. Much easier to use a cord or double length to quickly equalize and create a "master point" for the second to clip into. For true experiences alpine minimalists on double screw anchors using BD Turbo Express screws (two carabiner holes in hanger) I could understand using the rope... but that is the exception...
2) The easiest and best place to use the rope IMO is after topping out the climb when you are going to use a solid tree anchor anyways. Walk around the tree, walk back towards the edge of the climb, grab both strands a few feet above your tie-in, and make a doubled overhand on a bight to belay from. This simultaneously anchors you in so you can yell off belay and creates a convenient spot to directly belay off the anchor from, with zero gear. Guides use it all the time at the top of the route...
3) If you are swinging leads, then tying in with the rope can be fast and easy... or painstakingly over-complicated and slow... It takes quite a bit of practice to do it quickly, with the only advantage being you saved using your cord or a double length... for these methods I would suggest you read and practice what was already linked to:
http://www.rockclimbing.com/cgi-bin/forum/gforum.cgi?post=2590836;page=unread#unreadBottom-line, I definitely don't use the rope if doing all the leading (except at top-out), I "might" use it if swinging leads, but on a long route I prefer to lead in blocks, so I only swing once... It's good to know and practice using the rope for those times you come up short on gear... one more trick for you bag...
On a related note I think most people could benefit from learning to build equalized 3 point anchors with just a double length... by cord never leaves my harness with the exception of setting up a TR anchor on a big tree...