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Don't resize your cross. A 1px by 1px cross can't be sized down; it turns gray because it can't get smaller, and can't be sized up without the chance of it distorting (adding jaggies and the like) When selecting your layers to resize just avoid selecting the cross and you'll be hunky dory.

If you have to do this on many images and your cross is not on them yet, don't add it and use a batch script to resize all your images.

There's a good tutorial to do it here:

How to Batch Resize in Photoshop

If you're editing your images and not wanting to modify the document size I don't think there's a way to automate the resizing.

To center your transformation of all your layers. Select your layers, go to transform them (Ctrl+T) and hold (Shift+Alt+Click+Drag). This will use the mini cross that shows up in your transformation as the center point. You can position this cross wherever you like (even outside your selection) and it'll use that as the center.

Hope this helps!

Note: I am using Photoshop CS5