What customizations are you trying to make?
There are several changes you can make on an ibay-by-ibay basis using db variables (AllowOverride, PHPBaseDir, FollowSymLinks, Indexes, PHPRegisterGlobals).
If the change you want isn't listed, one option would be to create a custom version of /etc/e-smith/templates/etc/httpd/conf/httpd.conf/90e-smithAccess40ibays and add the code to read your setting from the db - then set the setting you need in the db for the ibay you want to customize.