Auto paint problems with basecoat\clearcoat?

I recently painted my 96 z28 the clear was chipping very bad so I sanded the entire car and shot it with BC\CC well it looked great until it rained the next day. it had deep blue waterspots under my clear I freaked out dummy me started tring to sand them out of the hood only thank god, it wasent doing any good so I had to work the next couple days the next day I was off I went out to look at it agan and the spots where all gone I was very happy they where gone but i still have to redo the hood because i went through the clear. I sanded the hood and shot another basecoat on it all around the spot I went to deep was wrinkeling up looked bad,I think it was because the solvents in the new paint caused the first base to soften, any suggestions I can solve this problem?????? Do u think if I sanded than shot sealer over the intire panel would help???