I'll take a stab at this. I use an MS Access MDE with a SQL Backend... but originally I had Access as the backend. It should work similarly. Though I do my client install manually without an install wizard due to the nature of our small business. However... I do have 5-10 users that use Terminal Server to run the MDE client.
After the user folder has been created:
C:\Documents and Settings\{account}
I create a folder for my application. This folder contains two files... a .cmd and .mde (the CMD does 3 things)
1) map a drive letter to the server\folder that is the location of the application
2) copy a fresh version of the .mde from the mapped drive
3) launch the mde
The runtime.mde has the linked tables to the backend database defined based on the mapped drive.
I didn't understand the last sentence of your post... "... how to use the mst transform" - so my suggestion might miss the mark. However... I've had much success running my Access .mde from client computers and Terminal Services using the .cmd attached. (and I just put a shortcut in their Users / Desktop that points to the .cmd )