Hi,
If there is just one line showing on 7940 phone, you should create a separate phone button template for 7940 with 2 lines. You just need to copy standard 7960 template and set 'none' for the last 4 lines. This way your users won't be able to configure speed dials for non-existing 7960 lines and 7940 template isnt accessable from the device profile settings.Specify this phone button template on the device profile for that user.
Then you need to copy 7940 standard template and create a new one with 2 lines. Next step would be going to Service->Service Parameters->Extension Mobility logout and changing "7940 phone template for EM Logout" to the template you just created, as the default one is standard 7940 with 1 line.