This may just be because I'm not the sharpest tool in the shed. But, I've tried for two hours now to figure out how to fix this problem:

When the logo is uploaded, it shifts only the center part down and causes everything to be out of alignment. can anyone please help me fix this! I want the bars to be lined up again and then I am going to try to make the rotating header images show up beside the logo.

The gray bars that span the entire width are a background image (See ATO>Body, Text & Links). To "move them down" you need to create a different background image.

aaaah. thanks, i can do that.