If you have a single server it is generally ok to do everything to make it work and do a full / backup. Only if you keep documentation of your actions (/etc/motd is good enough) . Altough messy,  mixing rpms/cpan/deb/custom builds is not _that_ bad unless you have to duplicate the machine. For example my personal laptop is a total dump:) Every time i do dist-upgrade somethings breaks but it's acceptable - i'm the only user.
If you have a couple machines that perform the same functions and you need them to perform very predictibable mixing different type of install modes will get you in a lot of trouble. You have to learn how to build rpms/deb and maybe set your own in-house yum repository.