1. No, all USB ports are available for loading system;
2. No, just choose the USB drive as first boot option;
3. The USB drive must be UEFI bootable when you create the windows installer usb;
4. I think the USB drive you created is mbr BIOS bootable, not UEFI. so it can boot from other system, not Jaguarboard.
Please create a UEFI bootable installer USB drive and try again.
BTW, it must be 32 bit windows.