There's two separate issue here. Some backs have a recess under the ground glass for a fresnel this means the fresnel itself doesn't alter the position of the glass, any shift in focus is relative to the depth of the fresnel rings rather than the overall thickness of the fresnel. There may need to be a thin shim when no fresnel is used.
However where a fresnnel moves the ground glass in a back not designed for a fresnel then the focus is altered and as Dan says in that case the fresnel should be on the rear of the Groundglass - pohotographer side. Where a back is designed to have a fresnle sandwiched on the inside of a fresnel (no specific recess) then when the fresnel is removed there needs to be quite a thick shim a touich less than the fresnels thickness.