Different Primary Links for Different Themes

Is there a way to make a single Drupal site display different Primary and Secondary links when a different Theme is chosen (in Drupal 4.7)

I have a site with 5 different main departments. They are all on one Drupal site, but each one uses a different Theme (which are basically the same theme but with different colors and header graphics) - using the Taxonomy Theme module. That seems to work just fine. Here's the problem:

I need each of the 5 different themes to have a different set of Primary and Secondary links. Each of the departments has a different set of section links on a horizontal navigation bar on the header, so I need the Theme for each department to use a different menu group as the Primary links menu as well as for the Secondary links menu.

More details on the situation: The 5 different themes are not actually separate themes: They're all in one Theme folder, within subfolders that have stylesheets in them to specify the right colors and background graphics for the header divs (using XHTML & CSS). These different "flavors" of the same Theme is done by several other themes I have seen, including B7, which has blue, green, and brown subfolders. (FYI, my theme is a modification I made to the Sharepoint-like theme, which supposedly utilizes PHPTemplate.)

So, I suppose the "different" themes could each reference a different menu in the page.tpl.php file etc. for the top of the page where the primary links go, but there are two problems with this:

1. I don't know what PHP code to put in to make it reference something other than Primary and Secondary. Can anyone tell me how to do this?

2. More importantly, since all 5 color flavors are in the same folder with different style sheets, they're all using the same page.tpl.php file etc. php files. So, is there a way to...

(a) as I asked above, make the Primary and Secondary menus use different menus of sets of links for different things?

(b) make the same PHP files reference different menus than the Primary and Secondary menus based on which theme subfolders is being used?

Figuring this out will allow me to finish my site. Thanks in advance for any help!