The most important concept to grasp is the Debian packaging system. In essence, large parts of your system should be considered under the control of the packaging system. These include:

For instance, if you replace /usr/bin/perl, that will work, but then if you upgrade your perl package, the file you put there will be replaced. Experts can get around this by putting packages on “hold” in aptitude.

One of the best installation methods is apt. You can use the command line version apt-get or full-screen text version aptitude. Note apt will also let you merge main, contrib, and non-free so you can have export-restricted packages as well as standard versions.

Alternative versions of applications are managed by update-alternatives. If you are maintaining multiple versions of your applications, read the update-alternatives man page.

Any jobs under the purview of the system administrator should be in /etc, since they are configuration files. If you have a root cron job for daily, weekly, or monthly runs, put them in /etc/cron.{daily,weekly,monthly}. These are invoked from /etc/crontab, and will run in alphabetic order, which serializes them.

On the other hand, if you have a cron job that (a) needs to run as a special user, or (b) needs to run at a special time or frequency, you can use either /etc/crontab, or, better yet, /etc/cron.d/whatever. These particular files also have an extra field that allows you to stipulate the user under which the cron job runs.

In either case, you just edit the files and cron will notice them automatically. There is no need to run a special command. For more information see cron(8), crontab(5), and /usr/share/doc/cron/README.Debian.