I am pretty sure that I didnt do this by "the book" but this is what seemed to work for me. My starting point was stock, single bowl system, with original distribution block.
I bolted the booster and master cylinder in place and ran my new line to re-connect the rear brakes. Rather than working around the booster and m/c, I pulled them back out to give me some room. Using the rear line as a reference point, I ran the other line working backwards from the distribution block, to the proportioning valve and then back to where it should connect to the m/c. When I put the booster and m/c back in, I got pretty lucky and with minor tweaking the brake line was in the right spot.
I did learn that if you take the bracket off the booster first and mount it and then the booster, it goes much faster.
With the booster and m/c out of the way, it also allowed me to get the connections tight the first time. Not sure how I would have gotten them tight if I left them in.