If they are stress cracks, then they are structural. If you can grind through the gel and see the cracks in the glass underneath (little white lines), then they need to be ground out completely and re-glassed. Then you need to figure out why it cracked to begin with (people sitting on the dash, inadequate support from a bulkhead, etc...) and fix that. Where are the cracks? Some pics would help. Anyways, unless the cracks are only in the gelcoat due to shrinkage, the repair method you explained will result in them coming back.
Just for information's sake, it has been my experience that repairing superficial stress cracks (those that are not getting worse, and not due to a collision) is a waste of time. Chances are that your will be chasing them for the life of the boat.....