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FX3 supports internal weak pull up/ pull down mode. You can set it by using the API CyU3PGpioSetIoMode(). This API make use of two arguments, one is the gpioid which indicates which GPIO pin to be updated and other is the ioMode which indicates whether it should be in pull down/ pull up mode. Please refer to the Page 312 of FX3 API guide for understanding more about this API. The FX3 API guide can be found in the following location:
C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\doc\firmware
Note: This path depends on the installation directory of FX3 SDK.
Also, you can understand the implementation by going through the source code of the API. This can be found in the file cyu3lpp.c which can be found in the following location:
C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\firmware\fx3_sdk_1_3_4_src\fx3_sdk_1_3_4_src\sdk\firmware\src\system
Again, the path mentioned above depends on the installation directory of FX3 SDK.
Please try using the API and let me know if you face any issues or have any queries.