Crutchfield is a great site to start with, so you can pick what's going to fit exactly. Replacing the factory speakers is going to help with the high's and mid's, and may even give you a little bass back especially if you've fried them and they're crackling.
I'd suggest you get the largest speaker that can fit the opening, instead of a smaller speaker that can be "adapted" to a larger opening. So if you're able to use a 6x8, and you're buying a 5x7 that has an adapter, you're downgrading especially on the bass-side of things.
If you're looking for a thumping, feel-it-in-your-seat kind of bass, I'd go with a separate amp and sub (or a powered sub). I wouldn't necessarily replace the stock sub, but rather wire in both and use all the power of the 2nd amp to run the sub. You're just not going to get huge bass out of the stock speakers no matter what you do with them (bass / low-frequency power requires a larger surface area in most configurations).