Hi Jack :)

If you want kind of transitions between two cylinders higlighted by Michael you can use Max SubD tools we have

Concept:



Stages



Result subdivided





You can set and mantain an exact diameter for cylinders,just transitions will be approx
Final object is a solid,so you can do booleans etc.
If you want to change the shape of transition just play with "polys" moving them until you get your target
If you are new here read this thread about SubD
http://moi3d.com/forum/index.php?webtag=MOI&msg=9689.1
file attached with all steps

M