I wish i could help, but i know nothing about screenpack codes. MGSSJ2 can help you i guess

I guess you can do this:
Make a custom box sprite like this:

The pink box must be the size of the black box and it must be just over it, and the pink color must be color 0(it doesn't display). The black color must be the color of the sky.
Then, set the pink box sprite with priority over the cloud sprites.
If done correctly, the black box must cover the cloud sprites, except where the box is, since the pink color doesn't show.

I hope you understand this... I'm bad at explaining things

You're wrong.
The whole sprite must have a size of 640X480, and the pink box must have the size of the black box, and it must be at the same position as in the menu.

Added (2010-02-11, 1:07 Am)
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Meanwhile,the main screen is not static,i mean cloud sprites,it scrolls.If ıt was static,i could do what you told me.