According to the built-in help, when you select Planar Align, you pick the part that needs to be aligned first and then select the face to which it should align.
When I try this in assembly, the second part moves to align with the first. In this assembly, I want to align the bottom header with the top, but the top header moves to align with the bottom.
Is the bottom one grounded or otherwise constrained in that axis? Unlikely you'd overlook that but I had to ask. You could ground the upper prior to your operation.
The bottom one is not constrained in that axis. When I placed the top one, I tried to establish a tangency relationship between the header body and the long vertical plane, but it wasn't a critical measurement so I just eyeballed it. Is it possible to do this (set a cylinder tangent to a plane)?
Yes, of course it's possible. And if it was really constrained in that direction then it shouldn't have moved. I set up a little assembly for test and it works as expected so I don't really know what you had going on.
The top wasn't constrained. Can you please tell me how I can establish a tangency relation between the pipe and the vertial plane? I tried the tangency opion in Assemble tab and also the Face Relate, but neither lets me pick the plane.