I think this is what you need to set to use filter offsets as for narrowband filters but the help is a little unclear. Are the settings below what you would change as opposed to normal “focus with filter being used” focusing? This assumes you have the correct focal positions already in the filter setup, of course.
When using narrowband filters and offsets, you need to check the "auto focus with filter" checkbox in the auto focus options dialog (and set the filter choice to a mostly transparent filter such as Luminance). You also need to check "Auto adjust focus per filter" on the main focus tab.