1) Install Notes off the CD with all the standard defaults except install the data drive to a common mapped drive where each user will store Notes data. e.g. o:drive
2) Make a folder called LotusNotesNotesini and move Lotus\Notes\notes.ini into that folder.
3) Write a batch file which will run on the first time that a user logs onto Terminal Server. This batch file should copy all the following files into the users data directory from the original data directory: *.ntf & *.dic.
4) From the LotusNotesNotesini folder copy notes.ini to the users winnt profile directory.
5) Log into Windows Terminal Server as a user and when the batch file has run you are then able to configure Notes for that user.
If you want to, you could program your batch file to look for differences between the original names.ntf and the one coppied to the user so that if the original one changes (because you have run an upgrade), new *.ntf file will be coppied over to all users to complete the upgrade.