Archie's Sonic X Series
Joe Edkin, the writer for the Sonic X series had the following to say about Knuckles' appearances in the series:

As for Knuckles in Sonic X, you will definitely see him in the series. He is prominently featured in issues two, four, and six (and appears in issues one and probably five). Sonic X (like the Sonic the Hedgehog comic) has a huge cast, so it's hard to feature every character in every issue.

Concerning the storyline:

Archie-SX will be tied directly into the TV show continuity (4Kids translation mainly). Unfortunately, because I don't get advance copies of the episodes, there will be a fairly long drag time between season 3 on TV and when I will be able to incorporate S3 elements into the comic.

The first six issues take place between episodes 32 and 33. From there, the comic series will move forward in time, weaving in and out of TV story arcs. Things that happened on the TV show will be reflected in the series and expanded on as we develop our own unique plots.

Concerning the Chaotix:

As for the Chaotix, I have proposed a storyline that could bring them back to Station Square for an indefinite period of time. I'd really like to have them to play with, but until I find out if the story is approved, I can't promise anything. The only concern I have is that we've already got a huge cast, so adding more characters to the mix makes it difficult for others like Big to have their chances to shine.

Source: Joe Edkin's posts at the Mobius Forum

Mike Pellerito Answers Sonic Fans' Questions
Not much Knuckles-centered information given (but there weren't many Knuckles-related questions asked), but if you'd like to see his responses, you can go here (Word or Text file version), here (thread at the Mobius Forum, here (Sonic HQ's News Page, or here (Ken's Message Board temporarily as all threads fall off the board depending on the activity of the board).