How do i change the position of the ad boxes?

How do i change the position of the ad boxes?

I would like the side boxes to be below the Header Rotating Banner.  Also, the side boxes are cut off on the screen, you can't see the whole box, only half.  how do i fix this?

And Three, can you make a box rotate ads in the same box.....?

Hello

If you are saying about default Dolphin's banners tool then you may try to use HShift, VShift, HShift, VShift during the banner creation. But if you want to completely move the ads blocks in different position then you need to modify HTML file of the template. 

Yes, it can be done by making custom modification for default banner manager functionality. If you are interesting you may contact me via internal mailbox to discuss the details.

Also you may take a look at My Banner 3.0 module which has the required features.