First of all, no, you can't merge all your masks into one. You can of course use a file with an alpha channel.
And no, there is no way to aim your adjustement layer on specific layers, you'll have to precompose. Precomposition will not have a huge impact on AE speed, so you can make a lot of them without noticing any speed change.
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There are a couple of options for you here. Probably the most effective would to to relight your scene like it was a real scene. Separate the bench from the background, create a wall and floor, make your bench, background and keyed actors 3D layers, add some ambient light and a spot light, then put a gobo between the spot light and the actors with the material properties set to cast shadows only. Then adjust the light transmission of the gobo and the values for shadow diffusion and light intensity to get the results you want.
The gobo could be created in Photoshop, from a solid with masks, with vector paint... just about any way you want as long as you get a layer with a bunch of oddly shaped holes in it. Without seeing your bench background shot I can't tell you the best way to separate it from the background and create a wall and floor layer to accept the shadows. You might want to check out Photoshop's Vanishing Point tools.
Here's a CS4 project I whipped up to demonstrate the technique of lighting with a gobo.
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You should not see pre-composing as a limitation or workaround, but rather a way of structuring your workflow and a means to control rendering order. There's nothing wrong with using it and contrary to your assumption, there is nothing that stops you from checking your result immediately. That's what multiple composition viewers and timelines are for. Just use the little lock symbol to assign a viewer permanently to a comp, then from the flyout menu in the top right corner add a second viewer. Multiple timelines can be created by simply arranging the tabs into separate panels. Assuming, you have the Synchronize related items option enabled in the prefs (it should be by default), that way whenever you change something in one comp, it will update in the other comp. Another alternative might simply be to use shape layers instead of conventional masks They do not really act liek a unified shape, either, but offer ways to merge and combine individual shapes plus have parametric animation options, which should greatly help getting exact windows, blinds or more random shapes. Rick's suggestion of using AE's 3D features is spozt on, but of course if you are really just worried of about transforming your shadow, using Corner Pin, Transform and other distortion effects might work just as well in combination with the Multiply blending mode.
Thanks a lot! I did learn a whole bunch of new things, yes I did. And I understand that I will not master After Effects the first couple of weeks.. What I learnt, and what was a milestone for me as an AE beginner, is that I can use an alpha channel bitmap to dictate how AF applies effects. That alone was worth this discussion.
What I did - I created a separate Comp with the footage from bench leaning against the wall (a wooden red wall). I then created an image in Photoshop, totally black, I then had a transparent background, and used the eraser with the shape of a leaf and punched many partly overlapping holes in it.
I then used this image above an adjustment layer, setting the adjustment layer's track matte to alpha matte. I added a brightness/contrast effect to the adjustment layer, reducing brightness by 33%. I also added a blur effect to the image layer with the leaves.
Now, I animate the image layer with the leaves, slightly back and forth, using the "Ease" option.
Having done this, I duplicated the two layers, to get the same effect a second time, but this time I changed the size of the "leaves image" slightly, and I animate it using a different direction and a different speed. This way I get two layers of leaves moving back and forth, and two layers overlapping each others partly using a random pattern. The result is so convincing, you won't believe it!
When it comes to lighting, I did make the layer with the couple 3D and I did use lights and I think it looks ok, but still I am not sure what I really did :-) There is a lot to learn here for me, obviously. Anyhows - the result, from starting with Keylight for the green-screen, through my latest efforts with the leaves, is way beyond my wildest expectations!
I am looking forward to my next "impossible task" which later will turn out to be routine for you expert guys who hang out here. I will study your posts later and see what I can learn more.