I need some advice. I would love a few expert opinions on the best practice procedures for using packages on Fedora Core 3 that are different versions than those that come from the default repositories.

The example at hand is this: The version of MySQL that comes with FC3 is 3.23, however, in order to use the fantastic MySql Administrator, you are required to use a 4.x branch package. What is the best way to install this package? I love being able to [yum update], but if I install this 4.x package from Mysql.com, it messes up my ability to do this. Also, the support packages won't install properly (like php-mysql), because it thinks that I don't actually have MySql installed.

Any tips are greatly appreciated.

I don't use yum on the ~30 RHEL3/FC2 systems I have. I change them over to apt-get and have all the packages the yum repositories should have.

yum or apt-get doesn't matter, really, right? I still have the same problem.

No, because if you use apt, you're pulling from the same repository for everything. Not the "here and there" approach you have now.