Normally when I replace the charge port on any iPhone or device I first connect it to the mainboard to test the connector. After I know that the charge port flex will connect and take amperage from the lightning cable. I leave the flex connector connected to the mainboard and proceed in installing the flex, with the motherboard first, Then I will route the charge port flex cable to the bottom of the phone. That ensures proper placement of the connector and also no kinks in the flex when applying it to the frame.
As for the microphone or any small component that needs sealant I use a liquid adhesive (no super Glue) use like T7000 T8000 or similar. Take a toothpick and dab a small amount around the area that needs adhesive. Then adhere to the 2 pieces( in this case the microphone to the frame. This always provides a water-tight seal. No matter the location.