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Most of your logs will be under /var/log and broken down into system logs, and those running by Samba and other services. Reading them, although a little boring, can be done using "less /var/log/logname". It pays to check through the system logs if nothing else to look for possible hardware failures (hard drive errors show in the logs with read/write failure usually long before the drive dies) and incorrect logins / possible attcks.
Although it's maybe a bit late now that the system is already live, tripwire or similar is also useful on servers to check for integrity of the files to ensure they haven't been comprised.
Also, even simple things like subscribing to the Debian security mailing lists is useful when managing servers so you see what security updates you will need to apply.
In terms of actually managing them, I'd recommend either physical console access at the machine, or via ssh. You could stick something like webmin on, but I wouldn't really recommend it as it simpyl adds another possible security hole and method of attackers getting in, something you always be trying to minimise on any machine, especially servers!
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