First of all there is no such thing as an antenna "tuner". The closest to that is the guy who trims a driven element to the resonance. You can "couple", you can "match", but not tune unless you change the physical dimensions of the radiating element.
An antenna is part of a system made along with the feedlines, coax, traps, etc. These are what must be dealt with by your transmitter. The mislabeled tuner is a box on the desk that deals with the reflected RF by "matching" energy from the transmitter to the mismatched load feedline and antenna. A "coupler” does the same. None of these devices "tune" the antenna.
With that being said, you are the one supplying the RF that RF goes from your final output stage to the coupling device, and on to the feedline then the antenna. An auto-tuner does not tune the antenna either, it cuts back the output power to a level that the final stage can safely tolerate. If you bypass the internal tuner and use your manual tuner, don’t use both.
Worried about the SWR? 1.5:1 = 4 w. Reflected; 2.0:1 = 11w. Reflected even a 3:1 SWR only returns 25 out of 100 watts. That 25 is, just like the others, burned up in the mismatched portion of the system. To grasp it - think of the power used by a train going along a straight track now think of the train going to the same point but around a hill to get there. The power delivered between the engine and the tracks requires more going around the curved route but the distance between the two points remains the same. Was the power lost? No, it was the same from the engine but the curve took that amount of power from the engine for a longer time.