That stumped me for a while, too. I considered laying track on top of the paper printouts, but that did not seem like a good idea. It would be better if I could somehow transfer the printed track plan onto the layout sub-roadbed.I'm still trying to determine exactly how I am going to lay my track over the brown paper drawings.
At first, I tried pushing pins or thumbtacks through the paper to make a pattern of little marks on the sub-roadbed beneath the paper. I found it difficult to make sense of a zillion little marks. Then I tried cutting away the paper a little at a time and marking the sub-roadbed as I went along. That was not very accurate.
Finally, I discovered that if I touched a Sharpie to the paper, it would bleed through the paper and leave a small dot on the layout. By placing dots at key points on the track plan, especially around turnouts, it became a simple matter to remove the paper and "connect the dots" using a straight edge and a flexible curved ruler: