You will have implement Async ADMux interface between FX3S and the Host Processor.
The timing diagram in the FX3S DataSheet (Fig.18 and 19) needs to be met. (The ADMux interface project is already given as example project in GPIF Designer. You can refer to same)
Please also refer to the following:
1. Section 9.1.8 of the App Note - https://www.cypress.com/file/201991/download
2. Referring to GpifToStorage example, you should be able to get CyFxAppMboxCallback() with the data sent from the Host Processor. As mentioned in the Point 1 please go through the mail box registers that you can make use of to communicate with FX3.
Once you are successfully able to communicate with the Host Processor then you can focus on the storage part.