I'm still not sure I understand the question. If a waypoint is on my flight plan, then yes I track it and make sure I go to that waypoint and I watch the distance and time go down as I get closer.

Example:
KATL
GEETK
VUZ
MEM
TIGGO
BITTY
KLAX

Taking off from Atlanta, the first waypoint on my flight plan may be GEETK, and that controller at some point (while on a heading after departure) say "Okay Air Shuttle, proceed direct to GEETK intersection and then resume own navigation" Meaning I'll turn to GEETK, and then once I reach GEETK I'll proceed directly to the Vulcan VOR (or whatever is next on my flight plan). While sometime enroute on the GEETK-VUZ leg, the controller may not have much traffic ahead so he could say "Air Shuttle cleared direct to TIGGO," meaning I will bypass VUZ and MEM and go directly to TIGGO where I will watch the distance and time go down as I get closer. They do this for shortcuts for us to save time and gas, or because we bug the hell out of them sometime for shortcuts (most of the time because I'm always late! haha).

Does this help you out at all, or was I just completely talking non-related nonsense?