Use of UBlox GPS data through an Ardupilot without the use of APM Planner

Hi everyone,
Sorry if this seems a question with an obvious answer, or if this is posted in the wrong section, but after playing with it for a few days I’ve had no luck.
The problem is that I would like to use the GPS data from a UBlox connected through an Ardupilot, but to upload my own version of Ardupilot software to it, using Arduino 1.0.5.
I was under the impression that to do so I would need to have the UBlox output NMEA data as opposed to UBX. Through the use of the UBlox passthrough firmware ( which is loaded through the APM Planner, and the u-center programme, I’ve been able to achieve this.
However when I subsequently upload software to other utilise this NMEA data, no data can be displayed. This is presumably as the firmware uploaded previously has been replaced, meaning that that UBlox can no longer provide GPS data outside of the APM Planner. Is there a way around this?
I’ve been trying to get this to work using the TinyGPS example code ( exactly as is, besides the changes of

SoftwareSerial ss(4, 3);

going to

SoftwareSerial ss(2, 3);

and with the baud rates changed from 115200 and 4800 to 38400.
The serial monitor displays the following once the code is uploaded:

Any help would be hugely appreciated.