All they have because "the novels say they do" is a relationship.
Janeway and Chakotay just don't work as a couple in my opinion. One of the main problems is probably that Chakotay to me has been little more than a cardboard cut-out character-wise for the majority of the series.
In the show, yes; in the novels, no. And I'm not just talking about the "Beyer-verse."
J/C elements have featured in a number of books, from Golden's work, to Carey, to Bennet, to Distant Shores
, et al.
In the show, Chuckles was hampered by lousy writing and Beltran's wooden acting. In the novels, at least in the ones I've read, he has none of these problems. Personally, I hated him in the series, but being privy to the character's "internal monologue" goes a ways in helping me not want to punch his tattoo back to the white, European, alien-gods he got it from.