You’d have to define a separate stylesheet for the admin BuddyBar, and hook it into the admin_head.
You can start work on that separate stylesheet, after you’ve done that I can help you hook it in the admin area.
Okay, I found an easier way for this.
Instead of creating a new stylesheet, you can use your existing admin bar CSS, but define some new rules for just the WPMU admin area.
Use this as your CSS selector:
body.wp-admin #wp-admin-bar {ENTER YOUR STYLES HERE}
Remember to define the body.wp-admin selector for each BuddyBar element you want to style.
eg.
body.wp-admin #wp-admin-bar {
background:yellow !important;}
body.wp-admin #wp-admin-bar li * {
font:12px normal georgia,times,serif !important;
}
This will change the BuddyBar background colour to yellow and the font to a serif for the WPMU admin area.
Hope that helps!