The Canberra 2016 amplifier/TCA modules have no external control for the input polarity. To change the polarity you must adjust some jumpers inside the amplifier module.
You'll know that you need to change polarity if you see negative peaks when looking at the amplifier output on an oscilloscope.
Turn off the power to the NIM crate.
Remove the module from the NIM crate - don't forget to disconnect the cables on the rear of the module, as well as those in front.
Remove the side panel of the module (the 'larger' side, which slides into the guides in the NIM crate)
The two jumpers JP2 and JP3 select positive or negative polarity. Both jumpers be set identically - closer to the module front panel for negative polarity, away from the front panel for positive polarity.
Shows the location of the polarity jumpers.
Replace the module side panel, reinsert the module in the NIM crate and reconnect the cables that you removed previously
Reapply the crate power.