I'm guessing coordinates in the instances?
What about 1 string instance, and 1 number instance to tell which tokenat is next in that string instance?
CoordinateX = tokenat(tokenat(InstaceString,InstanceNumber,"|"),0,",")
CoordinateY = tokenat(tokenat(InstaceString,InstanceNumber,"|"),1,",")
If instanceNumber=0 it will use the first set, if it's 1 it uses the second. (and if it's a top down game, you could have as many waypoints as you like.)
edit: You mentioned frame dependence, the Number instance could actually be the frame number.