The workgroup used at any given time Access is started it the last workgroup joined - unless the workgroup is specified in a command-line switch when starting Access.
Can you explain what you are doing with the Wise installer just a little more. Are you installing Access run-time files as well as the mde? If so, then include the system.mdw workgroup file with your installation. You could then include a desktop (or start menu) icon with the appropriate command-line to call the workgroup file - but Access should use the system.mdw file by default anyway.
If you are not installing Access run-time files, I assume you know each user must already have Access installed (the same version as your mde). In which case, system.mdw already exists somewhere on the workstation, but not in an entirely predictable location. To be sure, you probably should include the workgroup file with the mde (same directory) so you know where to point the command-line. If this is the direction you take, I highly recommend you rename your system.mdw file (and the command-line pointer) so that is is not confused with the system.mdw that was installed with Access initially.