OK, what I'm gonna do is tell you how I typically do it and then you can tell me if you think that would work for you.
For a 'new construction' window, which has the flange, you put the window in from the outside after you run a nice bead of silicon around the window flashing. Nail through the holes in the flange to install the window. I usually have a level ready and make sure the window is level/plumb (the sill should always be checked before installing but I check at several points along the way)
The window will now be at its proper location. At this point, the room/rooms should be drywalled, finished, and painted. The outside can also be sided. You just wrap the window with J-Channel and voila!
Now back inside. Go around to the windows and measure the distance from the window frame to the drywall (farthest point). Make sure that you check all 4 corners and round up. For example, a typical 2x4 wall w/ 1/2" exterior sheathing and 1/2" drywall can end up 5-5 1/4" thick. Depending on your window, you could easy have 1 1/2 to 2" for this measurement. This can get a bit confusing if you want to conserve material, but I'll try to explain.
If I was always getting 1 1/2" for this measurement, I'd get 1x4 stock and route an 1/8" round over on two corners (one common face). Then I'd stain and lacquer the two edges and the common face. That way, I could rip two extensions from that one piece. If you're not going to do all that work yourself, or are just going to paint the jam extensions, just order 1x4 stock and rip to size, discarding the waste. Also, if your measurements show that you can't get two extensions from one piece, just figure doing all of them with 1x4 stock.
Installing jam extensions is another post! Let me know if you wish to proceed and I'll follow up.
For flashing and other general installation on windows http://www.home-improvement4u.com/wi...eplacement.htm