copy your Setup folder from the cd. Replace the Setup.exe with exe from the patch;
run Setup.exe through terminal. It should be displaying: enter the cd to the drive; and
when you are going to play, enter the Emperor's folder and replace Emperor.exe with the same exe from patch.
As I say, I have not had any issues, so cannot say whether this will work.
I tried playing this with CXGames Linux 8.0.0 on my Intel 855GM graphics card (the old Centrino graphics card) with the -Intel driver and it would not even start (froze the system). Trying again with a "01:00.0 VGA compatible controller: ATI Technologies Inc Radeon RV250 [Mobility FireGL 9000] (rev 02)" (which runs the application fine in Windows):
the cinematics are pretty jerky and pretty unwatchable. (I tried adding the registry key 'HKCU\Software\Wine\Direct3D' and added key "OffscreenRenderingMode" (if it does note exist create it.), setting the value to "pbuffer", as suggested somewhere, but this did nothing.); and
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