My roommate read Darkly Dreaming Dexter after season 1 ended and he said much of the book is followed quite closely but with some differences. Season 1 was brilliant in every way. So far season 2 doesn't have the edgy writing, it has a slower pace and I'm not terribly impressed with some of the story lines. This could be largely because season 2 is not based on the books, it is original written material. I'm not hating season 2 but it feels "cranked out" to me. I believe there are two follow up books to Darkly Dreaming Dexter.
I thought season 2 so far is as good as season 1. I'm surprised they discovered those bags underneath the water already. I think that'll be this season's main story.