To begin with, you can load both samples and a VST onto the same instrument slot in Renoise. When you play it, it will trigger both.
But perhaps more desirable is the MIDI input, which let’s you assign the controller to specific instrument(s) and also define keyboard splits and more. http://tutorials.renoise.com/wiki/MIDI
Finally, I have created a tool which lets you customize things even further. It lets you use different layouts (isomorphic, chromatic etc.).
Not sure which pad controller you are referring to, but there is a number of them suppported out of the box: https://forum.renoise.com/t/duplex-keyboard/35159