Hi Daniel,
Sure it's possible either way.
Some explanation first:
The logo doesn't need a z-index at all, it's just nested into the header element and is only needed as a placeholder for the logo.
It's a bit overdone to give it a z-index of 20000. I don't know the meaning of this, with all my respect.
Flash headers, like on your page, are often given a z-index value to compensate artifacts and overlappings.
In this case, a z-index is respectable but again a value of 5000 is slightly overdone.
The z-index for the main navigation is also respectable. This has to do with displaying the submenu-items properly, if there are any. The value of 22000 is giving because the submenu-itmes must be visible upon the Flash header. So in this case the Flash header needs to be behind the menu-items and this is done correctly. However, I find a value of 22000 overrated but understandable in order to force the menu to display correctly. Since there aren't any submenu-items there's no need to force the menu to a higher z-index value.
What you can do are two things:
1) Adjusting your template's z-indexes according to the z-index for Ninja Shadowbox.
Safe z-index suggestions specific to your template are as follows:
#logo1 > no z-index at all.
#at-wrapmainnavigation { z-index: 998; }
#javascript-flash-header { z-index: 997; }
2) Adjust the Ninja Shadowbox z-index according to the z-index of your template.
Open up /modules/mod_ninja_shadowbox/ninja_shadowbox/js/skin/classic/skin.css.
Search for the selector (around line 36):
#shadowbox_container
And change the z-index value of 999 to 22001.
Like so:
#shadowbox_container { z-index: 22001; }
For both methods make sure you leave the structure of the other definitions within the selectors in tact.
Let us know how it goes.
Kind regards,
John