Master Switches

Just finished a panel upgrade on a Normal category (Not Experimental). One change made was to use PowerFlarm for GPS logging and glide computer. My master switch is a 3 position switch (Bat 1, Off, Batt 2). My old Volkslogger had no problem with swtching batteries as long as I flipped the switch fast, If I was slow it would reboot. Can I expect the same from the PF? I was thinking of wiring both batteries to one master or having two battery switches. I see no reason to use one battery at a time.
I bought the ship recently and it has much of the original electrical wiring and hardware (looks straight out of a German Home Depot). I initially purchased factory replacement electrical parts but they are expensive and not of very high quality. I wish to switch to Mil-Spec or higher quality for the master switch(S). Any recommendations? Discussed this with my IA and he has no problem with non factory stuff as long as it is aircraft grade (Which my sentiment also).
Thanks in advance.
Kirk