Depends on what you mean by configure. If you looking for configuration when compiling, you sure can with the customapache tool (search the forums).
You can also configure each domain's httpd.conf file with custom settings through the control panel from the admin level. You can also modify the template that is used for all current and future httpd.conf's in the /usr/local/directadmin/data/templates
Check out the readme file. Its been awhile , it might be in the custom directory.