I'm trying to create a solid part from 2 existing parts.  In the past I have used the "join" feature with success, but it doesn't seem to be working - at least not the way I want it to.  I make an assembly, and I do manage to succesfully join the 2 parts, but in my mind the whole idea behind doing that is to then save the assembly as a part file so that I can use the helix function (because I need to make threads) as well as other functions and features that are not available in assemblies.  I CAN do that - but the problem is that in the part file, I lose the ability to do an extruded cut, which I also need.  The extruded cut button is grayed out and upon sectioning the model, it appears to be hollow.  What gives?

I have done this in the past, but it has been so long that I can't remember how I did it.