If you are sure the battery is not faulty and the connector is seated properly you will need to try an update as the 6s sometimes needs one after a faulty battery.
· Have iTunes open on pc or mac with lightning cable connected just to PC.
· With the phone turned off, Hold the home button in and connect the cable.
· Wait for recovery mode to show up.
· Update the phone.
If this doesn’t work it will more than likely be a parts problem either battery or charge port.