milestones are interesting bits in the story. probably this means the group story, not individual player stories.
you track milestones encountered per day - the 'daily tally', and milestones encountered since the previous level up - the 'larger tally'.
when they rest, and begin the next day, their hp is restored, but the daily tally resets to 0.
have them add the daily tally to every skill roll. have powers that do different stuff at later milestones. later in the day you're running out of hp, but your abilities are more effective.
every 10 (or whatever) milestones in the larger tally, level up.