It is a little ironic that the shear volume of online-free tutorials on this subject creates its own obstacle to learning. If you have the time then take a look at fxphd.com if you haven't already. The volume and depth of what is covered there will keep you busy for the foreseeable future.
Joel Osis: https://vimeo.com/joelosis does a fantastic bob in his tutorials. The link is to his vimeo channel -it's all Flame/Smoke centric. But all the principles are there. They are condensed/short but packed with things you may never have known to exist but are from then on essential tools.
You are not specific on the software that you are using or want to use but you've mentioned After Effects which is a great tool especially for 2D. But if you want to combine 3D-assets & effects with 2D backplates you will be best served by a 3D compositing package. So again fxphd will get you going in Nuke, Flame, Smoke which are the packages that come immediately to mind. Lots of button pushes and shortcuts later....... These courses are taught by guys who are at the top of their game.
There are so many way to 'skin this cat' but do check out Joel's link above and dig through to the FBX compositing tips; the 3d tracking tips; the matte extraction tips; how to use z-depth and point-position passes; projection mapping.....the list goes on. Anyway apologies if you know all of this already, but still your request is still a little vague.
Good luck....
