Modules shipped in 2013+ (and many in the later half of 2012) have firmware that has been tested by simulation at the GPS factory at 40km.
You can tell what firmware you have by sending the firmware query command $PMTK605*31 (you can use the echo demo to send custom sentences to your GPS)
If your module replies with AXN_2.10_3339_2012072601 5223 that means you have version #5223 which is the 40Km-supported firmware version. If the number is higher then 5223 then its even more recent, and should include the 40Km support as well
HOWEVER these modules are not specifically designed for high-altitude balloon use. People have used them successfully but since we (at Adafruit) have not personally tested them for hi-alt use, we do not in any way guarantee they are suitable for high altitude use.
Please do not ask us to 'prove' that they are good for high altitude use, we do not have any way to do so
If you want to measure high altitude with a GPS, please find a module that can promise/guarantee high altitude functionality
Here is the binary of the 5632 firmware, you can use this tool to upload it using an FTDI or USB-TTL cable (or direct wiring with FTDI). We do not have a tutorial for updating the firmware, if you update the firmware and somehow brick the GPS, we do not offer replacements! Keep this in mind before performing the update process!
If you are using Leonardo (or Micro/Flora/ATmega32u4) or Mega, consider using a HardwareSerial port instead of SoftwareSerial!
Experimentation may be necessary to get the optimal results. We suggest RMC only for 10Hz since we've tested it.
The timezone cannot be changed, so you'll have to calculate local time based on UTC!