I use the embedded numpad on my compact (SMK-88 Blue) keyboard too, not for the numbers but for Mouse Keys. The newer TKLs and 60 and 75%s seem to have all given up on the numpad. Someone here suggested using the keynav program with a numpadless keyboard, but while keynav can move the pointer, and click, it can't "drag".
I don't know if there is a Linux program that will map the MouseKeys functionality to keys other than the numpad. Until such an animal is born, I have to stick with my older (circa 2007, 1KRO) model keyboard.