My group rationed out milestones based on the power levels listed in the book. We started at Feet in the Water (6 refresh, 20 skills), and the next one up, Up to Your Waist is 7 refresh, 25 skill points, so we had 4 Significant milestones (each giving a skill point), then one Major, (a point of refresh + a skill point.) We followed this same pattern up to Chest Deep (8 refresh, 30 skill points), then had to adjust the ratio a bit, as Submerged is 10 and 35. I think since hitting Chest Deep we've had 1 Signficant and 1 Major, so we're at 9 refresh and 32 skills now, then we'll have 2 more Significants before the next Major.
After hitting Submerged level, however, we may change things up again - we're not sure if we want to keep playing the same characters beyond that power level, change up the campaign, or what, as we've been running this game for almost a year now.