You need to edit your /etc/lilo.conf file and where you see the line:
change it to dos.
Then run lilo at the command by typing
That should fix the default boot OS.
About the Windows 2K and Linux, its different when using 98 to win2K, linux picks up and knows the dos image that 98 is on and automatically sets that up. with win2k, your gonna want to read the howto's in getting that to work, you can set it up to boot from either lilo or from the windows loader.