First of all the NEO 6 V1 is a very basic GPS with no external EEPROM and relies on battery backup to save settings, the battery on average will only retain these settings for @ 48hours, after which time the GPS will most likely do a cold start. With many Flight Controllers.. such as the Rabbit this gets around some of problem by configuring the GPS on boot and changing the baud rate etc.. but will still cold start after a few days without power.
The difference between the two is that the Neo 6 V2 has a bigger antennas 25x25mm and an external EEPROM which will hold settings on power loss, it also has a battery for warm starts like the V1, but again its quite small. Performance wise the V1 and V2 are exactly the same. The major advantage of the V2 is the external EEPROM which can be used to upload custom settings such ast the 3DR-Ublox.txt file specifically for the APM.