Refer to the Hardware Integration Manual (H.I.M.) document for guidance, and the Receiver Description and Protocol Reference for explanation. If you are a commercial customer of u-blox, you might request form u-blox a review of your design and implementation
VDD_VBUS is a sense input that indicates USB will be active. Yes, you should be able to connect VDD_VBUS to VCC at 3.3v as described in the H.I.M. Keep ANY 5V far away from NEO supply or IOs.