Use of UBlox data through an Ardupilot without the use of AP

Hi everyone,
Firstly sorry if this is in the wrong section, if I’m honest I’m not sure if this is a hardware or a software issue.
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.
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 ( loaded via 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 this a limitation of the hardware, or 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.

For once, I would use the FTDI-GPS adapter cable for the GPS instead of passthrough software - works perfectly and eliminates one possible point of failure.
Then… Question: When you changed the config of the GPS with uCenter, did you also save the changed config to the module’s flash? If not, after power loss, it will start with the old config again.
I have been tinkering with an uBlox module and an MinimOSD and I had no problems switching the GPS to output NMEA permanently.
Also beware that activating the NMEA sentences is not the whole story. You also have to deactivate the UBX sentences, otherwise they will keep coming and you might simply miss the NMEA sentences in the binary flood when testing.

Thank you for the prompt response!
So if I use the FTDI cable to access the UBlox and adjust the settings, once I upload something via the Arduino 1.0.5 software those settings will remain?
Or is saving it to the flash the thing that will make the settings remain, even if something else is uploaded?
Sorry I’m very inexperienced in this field.
I believe it was saved to the flash, as when the GPS is repowered and connected through the u-center NMEA is still displayed in the bottom right corner, as opposed to UBX.
I see, I’ll look into deactivating the UBX sentences as well, thank you so much you’ve already been a great help.

If you save the settings to flash, they remain IF NOT overwritten by another application.
IIRC, APM:Copter writes it’s own configuration to the uBlox at startup but does not save that to flash. That gave my quite some headache some time ago… I set the settings with uCenter, connected the GPS to the APM and the settings were gone. Connected back to uCenter, the settings were active again… :smiley:

Oh right I see!
So what I most likely need to do is write the uBlox configuration file into the application I upload myself?
Is there a way to do this? I played with this idea previously but the passthrough configuration file is a .hex file, so I saw it as a dead end.