I would suggest taking a two pronged approach.
On the Windows 98 side, start by installing some of the Open Source apps that are available for both Windows 98 and Linux, such as Open Office, GIMP, and Mozilla. This means that when your employees start to use Linux, they'll already have some familiarity with the applications. This will make switching less traumatic for your staff.
On the Linux side, start with the server. The keyword here is Samba, which is a program for connecting a Linux server to Windows file and print-sharing facilities. If installed properly, all the Windows boxes should connect transparently to the server.
I also think the IceWM windowmanager is good for people switching from Windows. You can pair it the Nautilus file/icon manager and have a very Windows-like combination.
There's a huge collection of files on the subject here:
http://www.grokdoc.net/index.php/Switching_to_Linux
Alex