GSharris,
I simply mask of the particular line that I am working with, fill the line with Porc-a-Fix using a microbrush (I am trying to limit exposure to the rest of the hull), allow each coat to dry before filling the line again (and again, and again, ad infinitum) until the recessed line becomes a raised line. Then, I sand it using fine grit sand paper until flush with the hull. I have noticed some shrinkage between fills, but it is a minor issue.
For those who would rather use putty, I found a better solution to Squadron putty. Try "Mighty Putty" found in the "Sold on TV" section of stores like Wal-Mart. It is actually a putty/epoxy mix that is easy to handle, dries quickly, and sands easily. It is far less messy than other putties and can be rolled safely and finely to fill any defect. It also dries in the shade of gray that Nagato is molded in.
I hope this helps!
Bill Morrison