If you have an amplifier connected to your transceiver output, do not use your transceiver’s antenna tuner. Even if your amplifier is turned off or in bypass mode don’t do it. The standing waves greater than 2:1 will potentially have high voltage nodes that can cause damage to the bypass components in the amplifier. Having relays or other components in the amplifier replaced can put a dent in your funds as well as your ability to work that rare DX.
If you have a high swr, say 5:1, use an external tuner at low power and get a good swr reading before engaging your amplifier.