You can set the touchpad to emulate third button by clicking left and right together. this setting is buried in the mouse configuration options and usually disabled by default.
There are two copy/paste buffers. The one you get with just the mouse is not the same as the one you get with ctrl-c ctrl-v. And frankly, once you know this, it's f*ing awesome.
If you really want a single buffer, there are apps that do that.
Godo