Ok for all those who have been waiting on this one - I've got the solution:
I will add more detail with screen shots and a video a bit later on - but the general gist of it is, I know there are dozens if not hundreds of people who want to get an APM in the air with one xbee transmitter, and have an Ardustation with antenna tracking on the ground where the Ardustation is plugged directly into a PC/Laptop and the only other xbee unit is plugged into the PC - well I've just figured it out.
The major problem most people come across with this is that the Ardustation is based on the ATmega328 which only has one UART, so it cannot be sending and receiving bia the XBEE directly to the APM whilst also transmitting data to the PC - which is how most people seemt o be trying to configure it. whereas with the same Physical connections I am using most people (including myself have been trying to get it working with Mission Planner - sorry but that just doesn't work.
The solution is QgroundControl.
These lovely settings above allow Qgroundcontrol to effectively relay all the Mavlink data it is receiving via the xbee-usb straight to the USB that the Ardustation is plugged in with. Effectively it is a MAVproxy...which I know a lot of people use specifically, but since no-one seems to be here sharing it I haven't really seen it as a solution.
So to recap:
APM with xbee 900mhz
PC with xbee sma in USB adaptor
Ardustation connected to PC using USB FTDI cable (no xbee plugged into Ardustation.)
This also has the Ardustation's FTDI cable correctly wired, as opposed to those making mention of needing the tx/rx lines swapped.
OK so why do I want this setup? Same as any of you that are looking at this thread I'm guessing, you want to use the Ardustation for an antenna tracker and also have the Laptop on-site for live Mission Planing, mavlink command sending and so on...
For me it is exactly that, and for those that say - but why would you bother lugging a laptop around...well my laptop is probably the least of what I'm lugging around when my UAV only just fits in the back of the FWD and my 28dbi 5.8ghz grid antenna will likely have to go on the roof (which incidently will likely be where I'll mount it anyway for ease of stability.
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Ok I've got a new solution, and it involves Mission Planner, not Qgroundcontrol.
It's even simpler than ever - will post the fix a bit later on - you're all going to love it. There will be a Simple Simple fix...and I'll put together a more advanced schematic fix when I get the chance.
Ok..No I can't wait.
The fix is simply plug your usb-xbee into the PC and wire a line directly from pin 2 on the xbee (d0) and pin 10 (GND) to the ardustation Pin 4 (which goes to D0 on xbee port and D0 on the atmega328 - funnt that...!) and the other (GND) directly to the GND port on the FTDI port of the Ardustation.
I'm going to put the entire unit in one box where I will actually de-track the Ardustation xbee adaptor (all bar the 2 required tracks, then place the whole USB module directly in the Ardustation, use the 3.3v line from the ardustation to power the USB-xbee, and use a USB cable from the PC to power the Ardustation, however that USB cable's data lines will still connect directly to the Xbee.
So the end result is Ardustation and MP receiving RX data in parallel via xbee, Mission planner using xbee for MAV transmission but Ardustation performing Antenna tracking onlly.
This image didn't upload in the original post - it's the Qgroundcontrol settings