Diagram: Black shape is base shape that I want the Blue shape to merge onto. I am guessing I can fix the way they bond afterwards.
I want to merge the two shapes into one so that they are no longer separate in Edit Mode. I then want to delete any hidden faces and maybe tidy up where the ramp faces meet the hexagon as well as delete the submerged base of the hexagon in line with the cylinder top.
Here is another diagram of what I mean...