Changing opacity in an adjustment layer to affect just one video track

Premiere Pro CS6
Hi,
I have a sequence of images in one video track that creates an animation and I've added an ultra key effect to remove the background of every image one by one (not sure if there was a better way to do this but anyway). Now I want to introduce this animation slowly with an opacity change but I can't seem to make it work. I've tried adding an adjustment layer and changing the opacity but this didn't work, I only want to change the opacity of this animation, not the other video track as well. So then I added a transform effect to the adjustment layer. I adjusted the opacity within this transform effect in this adjustment layer but I can't seem to make this work well either.
I've tried exporting the animation as a separate file so that I can bring it back to my project as one clip, but I'm a bit lost as to what kind of file to export it to. I tried an AAF file but that didn't load into my main project at all well and I had to force PPro to close.
Thanks.

Make your animation in its own sequence.
Then bring that sequence into the EDIT SEQUENCE.  ( a Nest)

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