Now I recognize you man
Ive been trough your website some good long time back...
The thing is, that Backup battery separate from cars circuit is possible, I've done it before and Im doing it again. Make a small and simple circuit board with diodes, relay and resistors, the major rule is to keep backup battery on charge along with cars battery when ignition is on/motor running, but not to transmit power back to cars circuit system from the backup battery and only to the alarm equipment connected.
separate relays on at least two separate alarms is not bad Idea, one relay for ECU power, other for coil power, or fuel cut,(note - u dont have to get second alarm wired to anything just to spare siren inside of the cabin and relay to i.e. ECU power,so if u park your car somewhere u dont wanna arm 150% u just use one general keyfob which does everything as major alarm system, and if you leave your car out for longer just hit the button on other keyfob to activate second alarm and cut ecu power off i.e.) and make few killswithches is important too, gps is no exception the probably most important if you want to hold on to what u have.
BR