Just make your header look like the one you have with Joomla. And then place it in your vB theme. We did something similar. We made our own plugin that puts the header on all sites. so when we change something in the header (that is running on his own sub domain) it is changed on all sites.
easiest way is to make your Header in dreamweaver or an other programme and put it in your vB template. You can use the guide to make your own custome header