Yes, Crosswire that is correct. Do all your work with the AR control set to 16:9.
FWIW I think it's generally agreed that you set up the 16:9 image first so that it fully fills your 2.35:1 screen heightwise and the side bars are the same width each side. Adjust the zoom, focus and manual shifts to achieve this and make sure the vertical and horizontal 'position' settings are at '0'. Then save this setting as 16:9.
Then, without touching the manual shift controls, use the zoom, focus and position controls to zoom a 2.35:1 image so that it fits perfectly on your 2.35:1 screen. Then save this as 2.35:1. If there isn't enough adjustment in the electronic position controls (usually if the projector is above or below the screen top/bottom) then you have to compromise: Use the position controls on the 16:9 setting in the opposite direction to that which you run out of adjustment in the 2.35:1 mode.If you have to do this, obviously you'll have to resave your 16:9 setting with this 'cheat'. Bare in mind that this will mean you'll cut a small amount off the 16:9 picture if the position control isn't at 0 (but it does remain pixel mapped even when moved above or below '0' FWIW).
Hope this helps.
"Don't believe everything you read on the internet". William Shakespeare 1615