The dll file is a requirement for some of the patches. It contains extra code that could not fit within the main executable.
The dll file (Moo3DLL.dll) needs to go into your main MoO3 directory to function properly. By default, that directory is:
C:\Program Files\Infogrames Interactive\Master of Orion 3\
If you are unable to find that directory, the game may have been installed somewhere else. Use the Windows 'Search' function and look for 'Moo3.exe'.
Often, a great deal of confusion arises over which dll version to use. This is because as new patches are released, the code for them is added to the dll. Also, patches may be updated, which require changes to the code in the dll. The best rule of thumb is to always use the most recent dll file. If, for any reason a patch doesn't function properly with the latest dll, check to see if there is a newer patch.