Yeah, I get that when spraying, just means it needs more paint there. But you need to do it while it's wet, or it won't be totally smooth. Just have to keep an eye out for those areas during the spray-painting process. Focus on painting once piece at a time, if you have too many going at once... you might overlook it.
I would let the it sit for a week to completely dry, and sand it smooth. After that coat it once more real good. The trick is getting it on thick, just before it starts to drip. Then let it dry for 3-4 days before touching it again.
And the weather also makes a difference in how your paint goes on. If it's real hot and humid, best wait till night when it's cooler. Cool and dry are ideal for painting.