Okay..let me see if I can explain it because it do become confusing.
First I create my banner in Admin/Tools/Banner Manager, assign it a banner group, and choose a photo from my H/D to upload. Your banner can be a photo or html text, but not both.
My Settings are:
Banner Status : Active
Banner New Window : No
Banner on SSL: Yes
Banner Title: My Banner Name
Banner Group: Banners All
Image: chosen from browser to upload to my store/images directory
Image Target : (left blank)
HTML Text: (left blank)
Sort Order-banner_box_all 0
Scheduled at: (left blank)
Expires on: (left blank)
Then I check in Admin/Config/Layout Settings and make sure Banner Display Group - Side Box banner_box_all is assigned to BannersAll (value). Then I go to Admin/Tools/Layout Boxes Controller and find the sideboxes/banner_box_all.php,
turn it on and locate it where I want it on my page.
I don't think other banners would show up in a particular box unless you assign
multiple banner groups to display in that box in your Admin/Config/Layout Settings.
Hope that helps!