Eve & Lilah are working for Wolfram & Hart to alienate Angel from his support system for W&H's own purposes. They are the ones responsible for sending the laptop to Buffy. Eve sent the demon after Wes (against Lilah's orders), and Lilah moved Spike out of W&H and put the memory spell on him. They are working together, but very much don't like each other and aren't playing nice. Eve was responsible for keeping Lindsey creating havoc in Angel's life.
Angel is debating an offer from Wolfram & Hart that would exchange Dana for Cordelia in some way. The details of this haven't been revealed yet, and he hasn't talked to anybody yet about it. That won't last too much longer, though.
Gemma is clearly more than human and dislikes Angel. She's interested in allies and has made an offer to Lindsey. Dana is pivotal to her.
Wes, Faith, Buffy, and Spike don't have their own agendas, other than their personal ones. They're caught in the tidal wave between these three factions, mostly because nobody has told them yet what's going on.
Dana's another pawn at this point. Poor girl.
Lindsey's original agenda is meaningless in the grand scheme of things. The importance of what he's been doing so far is primarily to bring him into Gemma and everybody else's circle so that the alliance with Gemma can get forged.
I think the most important thing to remember in reading Soul is that this, more than any other fic I've ever done, establishes that everybody has their own motive for doing something. The schisms of AtS S5 seemed like the perfect opportunity for me to play with this. Everyone always has their own reasons for doing something, and while often, the Scoobies and the AtS gang shared goals and motivations, that isn't the case in Soul.
Everything is fractured here. At the start of the story, people are pretty much islands. Spike is working on his own, Angel is still feeling slightly lost in the grand scheme, Wes is trying to adjust, Buffy is adapting to life in Rome, and even Faith isn't sharing the angst of her recent traumas in favor of bearing it alone. The same holds true for Dana, Gemma, and Lindsey. Lindsey *thinks* he has a partner in crime in Eve, but since she's been playing him all along, he doesn't. He's as alone as everybody else is.
The title is as much about W&H wanting Angel's soul, metaphorically speaking, as it is each person finding another to help them bear some of the load so that they're not alone. Buffy and Spike overcoming his failure to come to her. Wes and Faith overcoming their pasts. Angel learning that he has to trust someone at some point. Lindsey and Gemma...well, you get the idea. :)
I don't think I've ever done this for one of my fics before, but I know things are getting convoluted and I wanted to help if I could. I blame my love of 24 for the inspiration of all the Machiavellian maneuvers in this. If you've watched the show, you know that nobody is exactly who they seem and that anything can happen to spin the story in a new direction at any time. Ulterior motives abound.
Welcome to how I would've written S5, if I'd had the chance. ;)