Using GPS modules, remember they must be compliant to CoCom limits .
In GPS technology, you can find the term "CoCom Limits". This term refers to a limit placed on GPS tracking devices (like the modules used in the balloon payloads) that disables tracking when the device calculates that it is moving faster than 1000 knots (1852 km/h) at an altitude higher than 18000 meters (59055 feet). This was intended to prevent the use of GPS in intercontinental ballistic missile applications or similar.
Some GPS modules manufacturers apply this limit (disabling tracking) only when both speed and altitude limits are reached, while other manufacturers when either limit is reached. In the latter case, this causes some devices to refuse to operate in very high altitude balloons.
At present there are some GPS modules that may be used for tracking balloon flights. These modules may use an "AND" rather than an "OR" statement for their CoCom limits. This latter statement is preferable, since allows GPS modules to be used in balloon flights as they continue to function above 18ooo meters (60000 feet) as long as thet don't exceed 1000 knots speed.
The most interesting module for our purpose here is the newest in use: the uBlox 6/7/8 family, a 50 channel GPS in a SMD package, surface mounted. It is rated up to 50000 meters altitude in flight mode. Moreover, its an inexpensive module with good performance and it is available on ebay for € 8 about.
Ublox modules have their own binary protocol known as UBX but their modules also use NMEA. In order to power-up a GPS module, all that is reqired is VCC (+ Power), Ground and a TX line from the GPS module to the "flight computer", tipically an ATmega328P microcontroller.
When setting up a GPS module great care has to be made concerning voltage levels since many GPS modules run at 3.3 Volt and can not cope with signals that are higher.
One problem you might encounter with GPS modules is RFI (Radio Frequency Interference) generated by on-board microprocessors interfering with GPS signals. Typically this would exhibit itself as the on-board GPS not working with the antenna in different positions (particularly when the antenna is close to the source of interference). Any radio frequency generated near the GPS center frequency (1575.42 MHz) may be a real problem, particularly where this frequency is near some multiple (harmonic) of the transmit frequency.
GPS satellites orbit at 20200 Km - which means the line of sight distance varies from about 25800 Km as they come over the horizon down to 20200 Km if they are directly overhead. Correspondingly signal strength varies by about 2dB (a free space path loss of 182 to 184dB) while they are in view (assuming that the transmissions are omni-directional).
Another problem may be temperature: we must say that when GPS module got too cold, the crystals it uses drifts in frequency and therefore is unable to receive the GPS satellite transmissions. It is therefore recommended for long duration flights that there is some form of temperature control and that the flight computer code is capable of coping if the GPS module loses lock for long periods of time.
About the transmission protocol, it is NMEA, a standard protocol for communication with GPS Modules of a serial link. While it does not have many features it is implemented in all GPS modules however they often have their own protocol as well which can provide you with more information. Usually the connection is at 4800 baud 8-n-1 and there are a number of sentences transmitted containing different information.
 The Coordinating Committee for Multilateral Export Controls (CoCom) was established by Western bloc powers in the first five years after the end of World War II, during the Cold War, to put an arms embargo on COMECON countries. CoCom ceased to function on March 31, 1994, and the then-current control list of embargoed goods was retained by the member nations until the successor, the Wassenaar Arrangement, was established.