Since I'm the only person here who has read the stories in question I should probably toss in my two cents. I confess there's some hesitation because the Chanoran universe doesn't bear a lot of similarity to the KotOS universe. But that's likely to be more of a good thing than a bad thing. Contrast is good, right? Overall, I think tying the two universes together would be fine. Just remember that the KotOS Universe is supposed to consist of kid-friendly stories, but considering the fact that you were posting your stories on a LEGO message board I'm sure that'd hardly be an issue. :P However I must note that several chapters never made it through moderation; I assume that was on account of violence and too-specific weapon names, bearing in mind that I could be wrong. So long as you keep it PG it should all be good. Plus, if you put it up here I would get to keep reading it. :D :P
As for how it would be handled, I think you would continue writing it as a stand-alone story(what it is now). Then opportunities to have some characters cross into in Additional Manuscripts would start to show up, and eventually (eventually meaning sometime after SA) we could have them appear at some point in the main storyline. (That's what we're planning to do with Kal, after all. BWAHAHAHA- I've said too much.) Of course that's all just my initial thoughts, you've probably already thought of all this.