The new GPS for apm 2.6 has a mark “Front” on it. The mark has to be aligned with the APM board forward mark as mentioned. Now I Have two questions. One,
I have an old Ublox GPS module which has no mark on it. So is there any particular orientation while mounting this GPS module in my quadcopter? I mean how should I recongnize front side of these old modules?
TWO,
Is it possible to use the new GPS module with external compass, on APM2.5 ? I mean I know apm2.5 has an internal compass on it. But I want to know whether I can disable the internal compass and use the new GPS module with external compass on APM 2.5.
Could you post a photo of your ublox module? If it does not have an arrow it probably does not have a compass on it, in which case you can mount it facing any direction, as long as the antenna is pointing upwards.
Yes you can use the Ublox with compass with your APM2.5 board, you will just need to remove a solder joint on your APM2.5 board as shown below. The process is reversible, if you want to use the onboard compass again.
You can find more information about it here
Thank you … 
can you tell me something about the compass calibration like can I calibrate my compass inside my room? I saw two videos and I saw them calibrating it outside the room… Is There any particular reason behind that? and How I would recognize that my compass is been interfered by magnetic interference from motors and esc’s? what will be malfunctioning if the compass is been interfered? Thanks in advance.
It would be best to do it outside, but its ok to do it indoors too as that is just he initial calibration. During flight the ardupilot will constantly monitor and correct the compass interferance.