If you look at the announcement you can see in the comments that the APM should automatically detect and configure this GPS. (See for example the first comment on this page http://diydrones.com/profiles/blogs/new-3d-robotics-product-u-blox-...). So there would no need to select a GPS option in the MP.
Please note however that getting this GPS to work on an APM2.0 with a builtin GPS is much harder. You'd have to somehow disable the onboard GPS. It would probably involve cutting traces or soldering on an resistor. You can find more information about this in this discussion: http://diydrones.com/forum/topics/jumper-s-for-apm2-onboard-gps
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Is there a big difference between stock MTK (that is integrated into APM 2) and this u-blox LEA-6?
Virgis
If you look at the announcement you can see in the comments that the APM should automatically detect and configure this GPS. (See for example the first comment on this page http://diydrones.com/profiles/blogs/new-3d-robotics-product-u-blox-...). So there would no need to select a GPS option in the MP.
Please note however that getting this GPS to work on an APM2.0 with a builtin GPS is much harder. You'd have to somehow disable the onboard GPS. It would probably involve cutting traces or soldering on an resistor. You can find more information about this in this discussion: http://diydrones.com/forum/topics/jumper-s-for-apm2-onboard-gps