I beleive your referring to two separate things now. There are two separate things you want to do.
1. We will be releasing a updated version of vbgallery that turns off the vb
baseurl thing for vbGallery. Until then under your vbulletin options you can set the always use the baseurl option to NO.
2. For any links you have in your header navbar or footer you can in your vbGallery global options under the replacement options but the script names there. So for instance you have a script called member.php that script name should be under header replacements. By default in a normal vb
install we have all the normal replacements listed under navbar replacements as that is where they are.