You would put the SH4 v1.4 patch in the Silent Hunter 4 folder, where the SH4.exe file is, and run the patch from there. Once you have SH4 v1.3 installed, I think you have to start the game and "register" it with Ubisoft. Then exit the game, and you should be able to get the patch to "take".
If, however, you have the Steam version of SH4, then you cannot patch it with the Ubisoft file, and would have to purchase the Steam version of the "Uboat Missions" add-on, which would bring you up to v1.5, which is better anyway...
