The mmb-paste thing is called the 'yank buffer' (and it was a vi/Emacs feature that pre-dates clipboard-based copy/paste) - I use it extensively too, and one important thing to know about it is that it only works on text and it 'yanks' the text when you mmb, so the source app must still be running at the time.

I think it's great that there are 2 ways to move things around, but it does help a lot to be very clear on how both of them work, and some apps do things a bit differently too (eg Ctrl+C in Houdini can be followed by mmb in a terminal, which is a bit unusual, but ok once understood)