General queries about polygon pour - PCB Design
In general, polygon pours are used for ground and power rails. It depends on the layout and the requirements of the circuit. They are "just" copper and they can be used for many purposes: electrical connection, grounding, thermal relief, reference plane for a controlled impedance track, inter-plane coupling...

They can affect the performance of the GPS and BL as any other layout feature. They are part of the whole layout.

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Regarding your project, it sounds kind of complex PCB. 

Before thinking about polygon pours you should sketch a first schematics and then start to think about the PCB. 

Some questions that may help for the PCB design:


How many power rails do i need? 
What are the power requirements of each power rail?
Do I have a fine pitch packages like BGA or QFN? How many layers do I need to fan out these packages?
Do I need any controlled impedance track for the RF section?


Probably you would need 4 layer PCB and consider controlled-impedance tracks.