First, A CR2032 is NOT a rechargeable battery type.
Second, on the MTK GPS, these normally have a dedicated vbackup pin, so it will decide when to switch to the backup battery, no need to worry about V-in affecting it. You might have to cut a trace, but we would need a model number or picture to confirm. The current draw for the backup battery is <10ua's, so you really shouldn't need to worry about charging a cr2303 anyway, they will last for years at that rate.
Intersil has a technical brief on adding charging to a backup battery solution. http://www.intersil.com/content/dam/Intersil/documents/tb45/tb456.pdf It is related to rtc backups, but the idea is the same.
Essentially, either a regulator, or a resistor divider, connected through a blocking diode will provide a trickle charge circuit for a real rechargeable battery, and prevent it from draining out.
Both the datasheet you provided for the mt3339 chip, and this Application Note
http://www.auroramobile.ru/content/files/pdf/gtop/g6b/gtop_module_application_note_a00__mt3339_series_.pdf answer your question! Page 8, Section 2.1.2 Vbackup Battery
The MT3339 has a built in charging circuit, made of a simple blocking diode and resistor, from VCC. When regular power is applied (normally 0.3v higher than the backup battery), power goes through the diode, and powers the vbackup pin. At the same time, power goes through the internal resistor back into the backup battery. This prevents discharging, and provides a nominal trickle charge to the battery.
Additionally, the battery you mentioned is a LiR2032 battery. It is 3.6v, and while capacity varies between manufacturers, most datasheets provide a 35ma to 45ma capacity. It requires a 4.2v charging voltage for maximum charge. This would require a vcc of 4.3 or so.
And the math you are doing to compute how long the battery would last in a single charge is off. In perfect situation (no self discharge, constant output voltage and current, etc), 45mah / 7 ua is 6428.57143 hours, which is 267 days. But you need to take into account how the GPS module actually works with a backup battery. Since it has a internal blocking diode from VCC to VBackup, any time VCC is applied at (VCC + Diode Vf), the backup battery is no longer in use! So it will last significant longer, you know, if it weren't a rechargeable battery (datasheets show a self-discharge of 15% over 30 days after a full charge)
To compare, A regular CR2032 provides 200ma on average. This is 1190 days at constant 7ua current draw.