I would make everything you want to be in that small box inside it's own composition. This is often called a precomp. You could then create as many layers inside the precomp as you want for parts to fade in and out. So, if you have six buildings, you'd have six layers with a mask on each building. That way you can fade each building on and off as you wish.
Then, in your main comp, create a new solid, put a mask on it and use it as a track matte for the precomp so you can slide it around as much as you want.
It sounds like you're pretty new to AE. I would highly recommend getting a solid foundation underneath you (just like in construction). I'd recommend starting here: http://adobe.ly/AE_basics
That is the fastest free way I know to get up to speed on using AE. If you go through all the resources linked therein, you will know all about how to do what I suggested.
You are correct in assuming I am new to AE. Well, new as in I started about a year ago and never actually improve. I just keep solving my current 'problem' until the next comes along... then forget the initial problem lol.
I have actually been told not to even use AE, but use Premiere Pro but that would mean learning from scratch all over again.
I will try doing what you have said above and see what problems I come up with.
I promise to get round to going through those tutorials.
Szalam, now you have confirmed it is a mask I should be using can you explain something for me.
I have my original image/still filling the screen. I animate it so that the area (building) I want scales down and repositions top left. But then if I apply the mask to that one building it will actually apply to the whole layer so that the original fullsize image/still has this mask on. I obviously want it to change from full image to one building as it moves to the correct position.
Hope that makes sense.
I tried to explain how to do that in my first post. Try reading through it again.
Sorry if I am being a pain, but I really do appreciate your advice. I have done as you suggested and produced a video of my little pre-composition here which is pretty much what I was after... York Court - YouTube
The layers I used to create the composition are shown here in this image. I realise I have probably not done it the simplest way, but the result seems ok.
So I then made a new composition (main). I inserted this composition into the main one as you suggested. But I now seem to have got stuck. I thought you were saying to put duplicated comps in which I tried and modify each one to suit. But when I modify one, they all change.
I am sure it is easy from here, but maybe my brain has just frazzled a little doing the above.
Any clues please? Pretty please?
Scratch the world!
I think I sussed it without getting involved in the Matte thing. I was using the 'make composition from...' option when right-clicking my composition. This changed every composition when changing any detail. I am not sure what benefit that option has. When I used duplicate composition from the drop-down list, I could then edit the new one without it affecting the previous.
I ended with... Main Composition 1 - YouTube
Thank you again for pointing me in the right direction.
Glad you figured it out!