Well, I called Microsoft and there was a bit of useful stuff buried in a readme.txt that didn't seem to be on the April 2001 MSDN. The command line parameter SECURITYMODE=SQL seems to be a necessity for a brand new SQL 2000 MSDE installation on Win2K or NT. "sa" will be the only available login, and Windows aunthentication won't let "sa" log in. The parameters for specifying sa passwords don't work. After doing that, since I wanted to set up data table structures, I ran sqlserver.exe from the command line, minimized via the windows shell, waited 60 seconds and started feeding it SQL commands. If you want to coexist with SQL Clients loaded for other purposes, but still run your app's data off the local MSDE, you need to specify the instance name in both the installation and load command lines.

WSHShell = CreateObject("WScript.Shell")
ret1=WSHShell.Run(setuppath+'SETUP.EXE ';
+'INSTANCENAME="'+serverinstance+'" SECURITYMODE=SQL /QB',1,1)
ret2=WSHShell.Run('"'+programpath+'\Binn\sqlservr.exe" -s ';
+serverinstance,2,0)