First of all you need the following article
Basically because you can now assign usb devices to VMs, you need to stop the service that does so
You will then be able to find the usb under /vmfs/volumes after you reconnect it. You don't need to restart the service as you will reboot after the updates
Now put your ESXi in maintenance mode
Then to apply patches, use the following command
esxcli software vib install -d /vmfs/volumes/[USB]/[PATCH_FILE].zip
For more information go to http://www.chriscolotti.us/vmware/vsphere/how-to-patch-vsphere-5-esxi-without-update-manager/
Reboot when done and you should be setup!