Hi Brian:
Good news on the joist!
To install the roof boot just need to cut an oblong hole so pipe will stand up straight through the roof. Then you will slide the roof boot under the first layer of shingle and trim the shingle so it matches the contour of the metal/rubber interface... Once trimmed, the roof boot will slide into place and pipe goes up through hole in roof boot.
Can add a little roof adhesive or even silicone under the roof boot if want... but not needed if sits down tight to roof and shingle matches contour of bulge in the roof boot!
Let me know if that makes sense?
MARK