database application

What is more important; being able to sort and query employee information from the database in possibly esoteric ways, or easily inputting and displaying that information from the web?

If the former, you should avoid using CCK (and possibly Drupal entirely) and use a custom module which custom-builds the database tables in the way that will work best for your use.

If the latter, CCK should work fine.

It's important to note that using CCK isn't entirely intuitive at first. Well, even after that. :) Hence Garrett Albright's recommendation that you should consider a custom module if you need to query in an ad hoc or very flexible fashion. In either case, Drupal can be your home for this - but it will constitute a heavy investment if you aren't already familiar with its core principles.

I'd recommend starting with a Lullabot tutorial...
http://www.lullabot.com/articles/an_introduction_to_the_content_construc...
...and doing a really rudimentary install of Drupal + CCK / Views for discovery purposes. Views - when it comes to "complex" data querying - may or may not meet your needs, either.

In order to make better guesses, can you post some sample data structures and - more importantly - uses of these data?