Voltage measure problem in charge controller
You probably cant.

Since that mosfet is being turned on and off rapidly by whatever is controlling it, the controller probably reads the value during the off phase of the PWM cycle. As for time to settle, assuming the micro is controlling the PWM, it can take all the time in needs.

Your second schematic has a high side common, which though unusual, still passes the unloaded voltage reference to the PIC. 

In this case though the value is referenced to Battery voltage. That is "Battery voltage" means the solar panel is "dark". A lower value would indicate how much voltage the panel is generating. Since you would need to offset the value based on that reference it is a rather odd way to do it.