PokerTracker

Where can you make sure the colour defintion is only applicable to either mtt players or cash?
For eg. i want to tag cash players with less than a full 100bb stack a certain colour but obvioulsy that would be stupid for sng/mtt's...........Anyone??

The only way to accomplish that for now would be to base your color definitions on note definitions which have a filter for cash/tournament. However, you can't filter for current stack size in NC like you could using PT's Live Big Blinds stat so creating a badge based on current stack size is not possible at this time unfortunately

Can i not link it to a colour from the pokerstars noting system and not a badge?

PokerStars prohibits their notes file from being updated while you are playing, unfortunately. I think color coding by stack would be very nice but only useful when dynamic