You could do it that way, using a white background and making that transparent. Making white disappear is not trivial.
But "create separate motion clips for each element in the movie and then combine them in layers in after effects and using the transparency to get rid of the background information" is a highly unusual way to approach stop motion. You would only do it that way if your individual elements or characters do not interact with each other in any physical or implied way on your set. I think most of us would use a dedicated stop motion application with onion skinning and variable playback to an external monitor, create scenes with all active elements, edit the scenes together with music and sound effects and dialog in a video editor and use After Effects for effects and compositing.
Have you done stop motion before? If so, what made you decide to, or what about this particular project suggests that you try this approach?
So I guess its just to do with trail and error moving everything in the scene together?
Im completely new to film to be honest...
Im doing stop motion because it fit well with the brief I was given. Its more of a learning experience for me, I like things to look more hand made rather than digitalised.
Thanks for you advise!
You do not want to use After Effects for this project. That's like getting a double trailer semi truck to go grocery shopping.
INvestigate stop motion animation applications. Even those are not necessarily for beginners. If you hit youtube or vimeo, look for stop motion projects from other beginners. There are tens of thousands of them. You can see how hard it is.