Align can have several meanings here so I am not sure which way you mean,but I'll take a shot at it anyway.If the wainscoat is not meeting in the corner due to different heights then you didn't run a marker line prior to starting.If you're speaking about the ends of the wood butting against each other in the corner,then you need to read up on cutting angles for inside corners.If it's a different problem,please post.

It is the latter, a corner where they don't butt up correctly. I took over from the handyman who started, and he admired the problem for a long time before giving up. I don't know how you call a corner, but this is the one where if the chair rail extended out, it would be in the air, vs. the other corner of the landing, where the two walls meet to form the 90 degree angle.

Sounds like an outside corner.Both pieces of wainscoat come together by cutting 45 degree angles at the corner.Using a few pieces of scrap as a sample should give you an idea how to do it.

In addition to my last post,you have a second angle to cut so that the landing piece connects to the stair piece coming up at an angle.These double angle cuts are pretty tricky for the average Joe.Someone else may be able to help you along a little further.