travelling with 2 passports (dual passport holder)

I am very curious on how to travel using 2 passports...
I am a Philippine and BN(O) passport holder.
I am currently working in China, and planning a tour in Europe.
BN(O) passport holders does not need visa to enter EU.

My problem is how do I go about the check-in, immigration entry-exit etc. process....
I entered China using my Philippine passport with working visa pasted on it. In China, they do not recognize BNO passports. I also made inquiries and China will only put exit stamp on my Philippine passport. So there would be no exit stamp on my BNO passport.

Will EU immigration honor my exit stamp in my Philippine passport and grant entry using my BNO passport?