For some reason, when you select the entire scene in Scene Manager, transform buttons (X, Y, Z, W, H, R) are disabled. It is probably by design but I don't see any reason why they should be. I can still resize the scene as a whole using handles, but as I have been playing with building scenes a lot lately, I discovered that for high res scenes, when you apply it from a PSD file, it will be zoomed in so much when loaded that it requires a lot of scrolling to even find the handles. This is where the buttons would come in so handy!

Better yet, you could make the program even smarter by scaling the scene to the size of the project window automatically and if the user wants it smaller or bigger, they can then do it manually.