Using a LNBF 1000.4 as an example...If using the Sat Buddy and the battery is too low can I connect a cable from the receiver to the bottom connector of the Sat Buddy for power or will that put the LNBF into default mode??
No..
Instead hook up everything with with the receiver or switch being hooked to output one.
With the receiver of switch powered connect the Superbuddy to output 2 of the LNB then power on your SuperBuddy. You should now be able to do everything fine as the receiver or powered switch is powering the LNB.