APM Planner 2.0 or Mission Planner (1.2.9x)

Hi,
Im a little confused as to whats the offical sites and latest versions to use.

My Equipment/Hardware:
Hobbyking: Multiwii and Megapirate AIO Flight Controller w/FTDI (ATmega 2560) V2.0
UBLOX LEA-6H GPS Module w/Built-in Antenna 2.5m Accuracy V1.01
Multiwii MWC FC Bluetooth Module Programmer (Android compatible)

Setup/Planning/Tuning - Mission Planner:
ardupilot.com/downloads/

APM Planner 2.0 (2.x) » APM Planner 2.0 Windows
or
Mission Planner (1.2.9x) » MissionPlanner Installer


I have both installed but What i have found is that the Flight Modes do not seem to be compatible,
if i configure the flight modes in one, then the other does not recognise the flight modes that were set.

ie: i fire up Mission Planner (1.2.9x) and configure flight modes (say Alt hold) on position 2 of the switch, but if i then go into APM Planner 2.0, it does not show this change! infact all the modes seem wiped out.

Any help is appreciated.

Lee.

[wf]General copter software[/wf]
[mf]Copter/General[/mf]