I am sorry but I have no idea what you are doing from your description. Please give us a screenshot and reveal all properties of the layers in question. Just select them and press the u key twice.
I'm with Rick. From your description, it's impossible to tell what you are doing much less what you are trying to do. You can resize layers with their scale property, but I'm guessing that's not what you're doing.
Sorry, yes of course some images would help, here is a screen shot of a helicopter I have made in photoshop, the front layer I have called 'nose' (the bit looking a bit like a T)
Here is a screengrab of how I want the new helicopter to look:
So the front 'nose' has changed shape (and the rest of the helicopter but never mind that right now) and I was trying to morph the first shape into:
I read online that one way to do it is to put the path of the NEW Nose underneath the mask of the OLD nose, make keyframes at start of timeline for Mask Path and then copy the NEW keyframe and put it further down on the timeline along OLD nose Mask Path:
So far all good, the OLD nose turns into the NEW nose shape but the color behind stays fixed:
I solved it by not morphin and just turning down and up transperancy between the two different layers but using morphing would be so much better. The helicopter has got about 6-7 different layers and I would have to do it to each and everyone I think, but right now I cant even do it with one...
A mask is not going to change the shape of anything but the mask. Your technique is completely flawed. If the nose of the helicopter was a solid filling the frame then the you could animate the shape of the mask and keep the fill as the mask shape changes. Because your 'nose' has an alpha channel already and your mask moves to transparent areas there will be no color moved to the transparent areas.
To morph from one shape to another you either need to use the shape layers in AE and animate the path of the shape or use a morphing plug-in like Reflex. Here is what an animated shape layer looks like.
You could auto-trace your Photoshop layers or copy and paste the paths from Photoshop to a shape layer in AE and then pull the colors of the gradient fills from your Photoshop file.