There is no absolute need to place the .SYS and the .INF files created following the EZ LOADER design notes document in any particular folder. The .INF file that you have created is needed to associate the new driver that you have created (the .SYS file) with the device. But to make the process of associating the device with the new driver easier, place the .INF file in the same folder as the .SYS file and when the device comes up it is sufficient to point it to this .INF file wherever it is located in the system.
.INF -> C:\WINDOWS\inf
Both these methods will make it easy to bind the device to the newly created driver. The details on how to build the custom driver can be found in EZLoader Design notes.pdf which is available with the EZ-USB Devtools.The Ezloader folder contents will be available in folder C:\Cypress\USB\Drivers\ezloader after the installation of the EZ-USB Devtools available.