There are four ways you can configure the GPS chip:

• Without any backup power at all
• With a super-cap
• With a primary cell
• With a secondary cell

Turns out that the schematic for a secondary cell and a supercap are the same. For the secondary cell, the series resistor limits the charge current to just a trickle to avoid hitting it too hard.

Of course, the tradeoff between a supercap and secondary cell is that the supercap doesn't hold the power very long, while the secondary cell won't have a terribly long lifetime.

The primary cell probably is the most effective system. A CR-1220 cell will provide backup power for more or less the same period of time as its shelf life. The circuit is rather different for a primary cell. You use a pair of Schottky diodes with a common cathode connection (A BAT54C is ideal for this). The cathode goes to the VBack pin on the GPS module (with a 1 µF bypass cap). One anode goes to Vcc, the other to the positive side of the primary cell. As long as the battery voltage is lower than Vcc (the nominal voltage of a CR1220 is only 3 volts, not 3.3), this arrangement will prevent back-feeding power into the cell, and prevent the cell from powering anything except the VBack pin when the power is off.

The primary cell also offers the most flexibility. Adding the battery bail to the board isn't very expensive, and the GPS module will operate just fine with no battery installed. The voltage drop across the schottky diode isn't problematic - VBack is allowed to be slightly lower than Vcc.

EDIT: I've built a board with the battery backup configuration, and it works just fine.