[Jeff Hinkle]

If I’m understanding your question correctly, put the two layers into a Group folder, make sure the Group layer is selected in your Layers palette, make a selection from your third layer (CTL/Command-click its thumbnail), and then choose the align option you want. The two layers in the Group will move as one while maintaining their relative spacing from each other.

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It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

Ah, I see the problem. Try turning off your Gradient Overlay effect on your blue rectangle layer. That effect is being applied to both layers in the clipping group. Turn off the effect and your highlight layer should pop back into existence.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

Are the two items overlapping on screen? Option-clicking tells the top layer to only be visible where the bottom layer has opaque pixels. So if they’re not overlapping, the top layer will seem to disappear.

Also, if you have a blending mode on the blue rectangle, that will affect the color of your highlight layer as part of a clipping group. For example, if the blue layer is set to Multiply, and you make a clipping group with a white overlay layer, the white area will disappear.

If they are overlapping, can you post a screen cap of your work area/Layer palette? Maybe I can spot the issue.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

There’s a couple different ways to do it, if your highlight and blue rectangle are both on their own layer.

In the Layers palette, Alt/Option-click between your highlight layer and blue layer. That will create a clipping group of the two layers so your highlight will only appear where the blue layer is opaque. You can then link the two layers together if you want the highlight to stay in the same spot as you move the blue rectangle around.

If you don’t want to go that way, CTL/Command-click on the thumbnail of the blue rectangle in the Layers palette to create a selection the exact size and shape of the rectangle. Then select your highlight layer and add a layer mask (the icon at the bottom of the Layer palette that looks like a dark circle inside a white rectangle). Your highlight will be masked out in the shape of your blue rectangle.

And if you’re working with vector shapes and want to keep everything vector, select the path of your blue rectangle, copy, go to the Paths palette, select your highlight path layer and paste the new path into the layer (you’ll now have two paths). With the new rectangle path still selected, click on the Pen tool, and in the option bar along the top of the screen, set the path to Intersect Shape Areas.

One of those methods should do the trick for you.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

How big is the image you’re clicking into with the fixed-size marquee tool?

Are you setting the unit measurements of the tool to pixels and not inches?

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

If you’re clicking with the marquee tool in the 1000 x 378 image, then yes, it’ll just select the outer edge because your selection size is the same as your image size. Click in one of the original images you want to crop (I’m assuming they’re all larger than 1000 x 378) and you’ll get a selection the exact size you need. Move it to frame the part of the image you want to keep, and crop.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

Try this: In System Preferences, open Keyboard and select “Use all F1, F2, F3, etc. as standard function keys.” That should bypass the special functions printed on the keys.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

Select your Gradient tool (hit G on the keyboard if you can’t find the tool icon). Notice the toolbar across the top of your screen has changed. On the left side there will be a small representation of the current gradient, which is most likely your foreground color to your background color. Click on this gradient swatch and a drop down menu will show up with all the current presets. The second preset (unless you’ve changed them) should be Foreground to Transparent, which will be your foreground color fading to a gray checkerboard pattern. Select that one and set your foreground color to white.

Now click where you want your gradient to start, in this case about 10 pixels above the top of your selection. Keep the mouse button held down and drag to about 5 pixels below the bottom edge of your selection (holding Shift will constrain your drag to a straight line). Release the mouse and your gradient will be created.

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

What weird temporal properties are you getting? Bringing a layered Photoshop document into After Effects will generate a comp with each layer having its own set of properties (Scale, Position, Rotation, etc.) but they should all be set to their defaults with no actual animation. Was your original PSD document just a plain layered image, or had you imported video, or done some animation through Photoshop Extended’s timeline?

—
It is easier to destroy than to create.
More fun, too.

[Jeff Hinkle]

Almost forgot: Don’t forget to make a new layer in between building your selection and dragging with the Gradient tool. That’s the icon at the bottom of the Layers palette that looks like a little notepad with the corner folded over. Then when you drag with the Gradient tool, your gradient will go in this new layer and not on top of your existing image.

—
It is easier to destroy than to create.
More fun, too.