Installing outside prefix

Hi I am trying to make a port with gutenprint (was gimp-print) and it will install a lot of stuff outside of prefix because if its relation to cups (in /etc/cups, /usr/share/cups and /usr/libexec/cups). Now I don't think I can just put everything inside prefix unless I create a cups port which would be just creating another kind of problem. Now, I am tempted to think it would be better to NOT create such a port. Any advised and enlightening opinions on this ? thanks yves