I finished watching Buff and Angel some time ago and loved it! I feel like it's time for more so I want to get into the comics. Particularly Buffy's Season 8 and 9 and Angel After the Fall. In what order should I start reading them? Is there a lot of crossover between the two series? What about the other ones like Spike After the Fall and Fray (I know this one is set in a very distant future, but I've heard there are some references to the mythology established there in the modes day comics).
The comics are a bit complicated because IDW developed the post-Angel storyline, and Dark Horse developed the post-Buffy storyline, and they were meant to more-or-less keep to their own characters. Angel, however, is an important part of Buffy's Season 8, and to keep the peace Willow appears in (IDW's) Spike, so there is some crossover.
In "Slay the Critics" in Buffy Season 9 #5, we're told:
So there are some continuity issues (and maybe more to come). I think this means it's reasonable to skip all the IDW's comics and go straight to Dark Horse - at top-level (i.e. Joss) canon, the Dark Horse comics are what matter, and the IDW stories are lower-level backstory canon.
And from "Slay the Critics" in Buffy's Season 9 #1:
The Angel and Buffy the Vampire Slayer Classic comics take place before and during both of the TV series. These are fairly standalone and while they provide a little more background, it doesn't really matter what order they are consumed in. I'd leave these until after you're well into Season 8 (since they stand alone, you can intermix them whenever you want something more) since they're not as compelling.
My suggestion would be to read them separately, either Angel or Buffy straight through. Personally I would (and did) start with Buffy. Once you're caught up with that, I'd do the same with the Angel series and then read each as they're released. There's very little cross-over between the two. I believe Spike: After the Fall fits into the Angel sequence - according to Wikipedia it falls after issues 6-8 of Angel. Wikipedia also shows the Angel/Spike/other spin-offs publishing order, which is usually the sensible order to read comics in.
Fray has a cross-over in Buffy Season 8 but you don't need to read it beforehand (I know I didn't, and while it lead to a bit of confusion the fact that you know of its existance means you're better prepared than I was).