The icon used by waypoint markers is defined from within MapSource itself, you can set the default icon for waypoints here to whatever you like by using: Edit -> Preferences -> Waypoint, then selecting the waypoint icon you desire.
If you don't like any of the standard icons, you can select your own by following the instructions here:
If your MapSource Map has too many Waypoints on it
If you're talking about the chequered flag at the end of a navigated route calculated by the Zumo unit itself, I haven't yet found a way that this can be changed (although I imagine that would mean changing one of the compiled files on the unit itself)
HTH.
David