Do I need to shoot at ISO 6 or 12 with the filer on? No. I rate it at ISO 200 (DX default so no need to change camera settings) and use a deep red filter (Hoya 25A) and let the camera take care of the exposure.
Do I need to also set exposure compensation as well/instead? Nope, leave it to the camera.
What is best way to focus, manual or automatic? Using a red filter I can see enough to focus
I intend to shoot landscapes/panoramic so would normally go for F11, is this the same for SFX 200? Yep

Strictly speaking, SFX is not a true IR film but is more sensitive to IR wavelengths. The EOS 3 will fog true IR films because of the IR counter it has, but SFX is perfectly safe to use.

Here's one I produced with my trusty Nikon FM2: