Are you keeping your factory pump aswell? If not, just remove it and place it where the old one was. Use barbed fittings and fuel line clamps, not hose clips. If you don't know what I mean I will snap some pics later on.
As far as filter goes, having it before the pump will save it from any major rust breaking off, but if you are not running an intank pump, priming the new filter will be a bitch.