[Sebaplatz]

I’m a newbie too, but i can recommend you rendering in numbered TIFF files with a SEPARATE ALPHA channel also in TIFF.
You can do this by going to the RENDER SETTINGS (ctrl+b), then SAVE. On the SAVE settings you can specify the type of file that you want for your output.
Select TIF in the file type and assign a folder specifically for the render.
Below that you can see a box that says ALPHA CHANNEL; Select it.
Then a box that says SEPARATE ALPHA; Select it too.
Then hit Shift+R or RENDER(menu)>RENDER TO PICTURE VIEWER
You’ll have a bunch of numbered TIFFS and another bunch that has the “A” prefix in it’s name. Eg: Render_A_01.tif or something like that.
the A files correspond to the alpha channel for every frame.

By rendering each frame in one file, you can prevent rendering the whole bunch again, in the case that you’ve made a mistake.

You can import both bunches (alpha and content) to after effects as a sequence. Then, you can set the alpha track to be an animated matte for the track that you want to be visible (defines transparent areas for a track).