You can connect the USB VBUS from the Computer to the VBUS pin of FX3 and the output of the LDO to the VBATT pin of FX3.
Connecting VBUS of Computer to VBUS of FX3 enables VBUS detection in the PC side when FX3 is connected or disconnected. The PC will know whether a USB device is connected or not.
If both the VBUS and VBATT are powered, Fx3 by default takes power only from VBUS pin. So, in your case, you need to tell FX3 to draw power from the VBATT pin (LDO) and not from VBUS pin (Computer).
So, you need to call CyU3PUsbVBattEnable API in your firmware. You need to call this API before the CyU3PConnectState API.
For power consumption estimation, please refer: