Thanks for the response Marcus.
I figured it out yesterday. Looks like DB2 v8.1 still has the same command, DB2CFIMP.exe. I just went through the configuration assistant, then exported the database into a file. Then I just ran DB2CFIMP.exe and specified the exported file and it configured the databased! I read through tons of posts here and discovered that the imp in db2cfimp means import. I guess I failed to specify that i didnt want to launch the configuration assistant and use the import option in the menus. Now I can just use the following command to do the configuration:
"c:\program files\sqllib\bin\db2cfimp.exe" "%SrcDir%\whatever folder\database configuration file"