If you insist that one CO2 tank be depleted before the other, so you can refill one at a time, then do the following:
Each CO2 bottle gets its own regulator. Primary bottle regulator should be set to 100 PSI
Backup bottle gets set to 65 PSI
Give each line from the two bottles a check valve and then tee the two bottle outlet lines together, to make a combined outlet. Feed that to the inlet of a third regulator. Set this regulator to something like 35 PSI or whatever you need. Connect solenoids, bubble counters, whatever you want, to this supply.
The first bottle will deplete completely, first, and then once it is drops below 65 psi, the backup bottle starts to dispense. At this time, you can completely disconnect the primary bottle and get it refilled. Once you do that though, you should make your backup tank your new primary tank, since you have already started using it, and you want to keep the newly refilled bottle as backup. To do this, you swap the regulator setpoints (100 and 65 becomes 65 and 100), the third regulator doesn't need to be adjusted.
Make sure you adjust setpoints while you are flowing gas, or you will make a mistake.