Hi Matthew,
if you are using a standard flight plan you can use the GeoInit block to call ResetGroundReferenceHere() which will set your current altitude as ground alt and move your waypoints by the difference to previous ground alt.
Depending on which paparazzi_version you are using, setting of the barometer scale (pressure to meters) differs.
On v5.0x you still have to set INS_BARO_SENS, whereas on master the baro outputs pressure in Pascal and the proper barometric formula is used to convert it to an altitude in meters.
Regarding logging: if you start a session that includes a server (normal flight session) you don't have to start an additional server process. Make sure it is not running with the -n (nolog) flag. Then switch to the raw telemetry, so your autopilot will actually send the raw sensor readings. You can also run the messages tool to see if you receive the RAW messages for the sensor you want to calibrate. Stop the server so it will write the log to disk.
Then when you have a log with the data, call the calibration script with the -s SENSOR as described
on the wiki, so e.g. for the accelerometers:
sw/tools/calibration/calibrate.py -s ACCEL var/logs/YY_MM_DD__hh_mm_ss.data
Cheers, Felix