Since you installed both versions, teh correct versin should have been installed on your current server. To verify that your Domino server is now at the correct level, run the command "Sh Server" from teh domino console. This shoul verify thatthe FixPack 2 was installed.
Installign the verson for the incorrect archetechture of Windows (i.e. 32 bit or 64 bit) should not interfere with the corectly installed server.