If you turn off WiFi, Bluetooth, or GPS in the settings, then the OS will automatically power down the circuitry. No need to do anything else.
As a side note: If you are designing your own PCB, you must be VERY careful with the circuit layouts, particularly the power traces and the high speed connections. If your CAD tools cannot simulate signal integrity and compute impedance vs frequency plots of the power traces the board will not work. Please read the APQ8016E design guidelines https://developer.qualcomm.com/hardware/snapdragon-410/tools
A better way to do this is to buy a SOM (System On Module) that is already tested. Checkout the SOMs from Intrinsyc, and InForce Computing. The SOM will be significantly less expensive than the set-up costs for a 8 to 10 layer PCB.
Full Disclosure: I am an employee of Qualcomm Canada, any opinions expressed in this or any other posting may not reflect the opinions of my employer.