Why do the fuses keep blowing on my amp and my sub is not working?

Sometimes it takes alternators and batteries a few days or so to break in when you replace them both at once. But as for the fuse thing, you might have a break in your wire, or just a bad connection/ground somewhere. Remember, you can always put higher fuses in something that only needs a smaller one. Ex. like a 30a fuse in a holder that requires only a 20a. It makes the fuse less likely to blow and it'll last longer.