We seed at 7lbs / 1000sqft.
After a month or so we "second seed" at 3.5 lbs / 1000sqft.
I have a few questions re: seed only coming up in the holes;
1. What is the soil type?
2. How was it watered?
3. Did you "scratch" the surface well?
I find that when seed germinates and grows only in plug holes it is generally due to a dry soil dominated by clay, that isn't watered well following seeding.
I would re-seed about 4 weeks after the first application. Start by watering until you see puddling. Then use a star rake to break up the soil, in bare areas, so that it looks like cottage cheese (Star rakes/ Weasels break up the soil well without uprooting existing grass...too badly). This should prep the soil nicely for your second seeding. I would apply as stated above about 3-4 lbs / 1000sqft, while going heavier on bare areas. Water once a day for 10-14 days just until puddling begins after seeding.
Hope that helps.