Coming through in places are likely to be because of high and low spots in the steal surface. Use a guide coat then possibly a foam block. This will help show you were they are then you can split the difference with your sanding technique.
Using sand paper and just your fingers often exaggerates this problem.
How to Apply Guide Coat for Car Restoration: Classic Car Restoration: Body Work | eHow.com
This should shed light on what I am trying to say. Cheers