I've started to create some drum maps for some Kontakt instruments and a bit bemused with the differences as what is considered C2 in Kontakt and Kontakt ((Same problem applies with EW Play)

Are there any helpful hints in regards to this?

Also, are there any benefits to the input / output mapping that I may not have thought of (best practise).

See Base Octave for Pitches http://www.cakewalk.com/Documentation?product=SONAR&language=3&help=0x22B06
 

Handy to know that.... bu does changing this setup mess up the existing drum maps supplied by cakewalk (and others)?

Changing the Base Octave for Pitches does not affect MIDI note numbers. Drum maps create relations between user defined names, inbound and output MIDI note numbers. Changing the Base Octave for Pitches changes the note name displayed next to the note numbers in the Drum Map In and Out Note columns but does not affect the existing entries in the Name column.

Thanks Scook!