I'm surprised that I'm having trouble remembering when they wrapped up the Matthew Morgan thing, but Laura moved into his by-then-vacant house after she turned up in Collinsport, so MM was fully a part of storyline one, only. So Storyline #1 was Roger vs. Burke plus Matthew. Laura was DS storyline #2. DS storyline #3 was Jason McGuire/Barnabas.
Wait, Matthew may have bled into the start of Laura just a little bit, because she was called upon to react to the news of his end, maybe, and despite having presumably known about him in the old days, she seemed to have no opinion. So I think MM's culmination went on between Laura's first scene and her moving onto the estate. Either way, he was gone for months before Barnabas is even spoken of.
Dr. Julia Hoffman was called in as a psychiatrist to enable Maggie to get her memory back about the time she'd spent as Barnabas's prisoner, so the Barnabas story was well underway and cooking before Julia was a twinkle in the writers' eyes.
They say Alexandra Moltke left because they weren't doing anything with her character. If she had known a definite end was coming soon, presumably she'd have finished things out, but who knows.
I believe there was just one scene involving Vicki (#2) and Amy. Vicki comes into the bedroom of one of the kids, while David and Amy have just started making contact with Quentin. There may have been a second scene, I'm not sure.
I presume you don't care about spoilers, just because you ask all this in the first place. I'd be grateful for an incomplete memory, if I were you. It makes re-watchings more enjoyable.
