Are your countersunk holes located using position tolerance? If so the countersinks are already related to the hole diameters within the positional tolerance used. If you've toleranced the mating parts properly this level of control is typically adequate.
Are you sure the countersinks are off from the holes, have you confirmed this?
If the mating part has a pattern of threaded holes that the screws are going into then you may have another problem causing the screw heads to appear out of true with the countersinks.
Because of the cone shape of the countersunk they tend want to center the screws to the countersink. Threaded holes also tend to center screws in them due to the geometry of the thread. So you have 2 competing features trying to center the screws, this is called a fixed-fixed fastener situation. Unless you match drill the pieces it's very unlikely the countersinks and threaded holes will be very closely lined up, they will be off by a few thou' most likely. This in turn will cause the heads to not sit flush and/or create stresses in the heads which in some circumstances may cause them to fail.
So to avoid this:
1. Avoid fixed-fixed fastener situations where ever possible. When heads protruding are not acceptable consider counterbores with another type of screw. Button heads have a fairly low profile and can be counter bored flush into relatively thin material.
2. If you must have fixed-fixed fasteners then there are steps you can take to ensure the head is always flush or below flush however, IT DOES NOT PREVENT INCREASED STRESS IN THE SCREW HEADS/MATING PARTS. Essentially you can oversize the countersink so that even when the screw head is off center to it, it will still sit flush. When using positional Tolerancing, which is usually the most appropriate way for hole patterns, you can use the below method.
Use the tightest positional tolerance on both countersunk holes and threaded holes that you can get away with from a manufacturability/cost point of view. Threaded holes are difficult to hold very tight but countersinks can be held fairly tight with less cost increase. Add the total positional tolerance of the two holes to the minimum diameter of the countersink. This will ensure the screw head is always flush or under flush.
For example, say your threaded holes have position of dia .005 (which is about as tight as I'd want to go for a threaded hole and will probably increase cost). Say your countersunk holes have a position of dia .003 (again fairly tight with a possible cost impact). So the total position is .003 + .005 = .008.
For a #4 socket flat head screw I believe the max sharp head dia is .256.
So you would want your minimum countersink dia to be .256+.008 = .264.
However, as mentioned above, this may still cause stress in the screw head and the countersunk part.
Posting guidelines faq731-376 (probably not aimed specifically at you)
What is Engineering anyway: faq1088-1484