All you should have to do is add two lines to the setup.ini file that is in the same directory with the setup.exe.
You setup.ini should read something like:

[options]
TARGETDIR="C:\Program Files\Microsoft SQL Server\"
DATADIR="C:\Program Files\Microsoft SQL Server\"

Of course you should change these to the directorys you want to use.

You can find more information in the readme.txt file that is in the same directory with setup.exe.

Hope this helps.