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 of apt as well as tools like aptitude or synaptic (which are just graphical frontends for apt). Note that apt will also let you merge main, contrib, non-free, and non-free-firmware so you can have restricted packages (strictly speaking not belonging to Debian) as well as packages from Debian GNU/Linux at the same time.

There are official and unofficial software repositories that are not enabled in the default Debian install. These contain software which many find important and expect to have. Information on these additional repositories can be found on the Debian Wiki page titled The Software Available for Debian's Stable Release.

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 account 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.