Should be slightly below or flush. If you go in TOO far, it can block the oil passage.
Are you sure the seal is leaking? Sometimes it can be the paper gasket for the rear main bearing or even the breather tube gasket. If this is a loop style breather box with the return line, the short rubber hose can allow oil into the bell housing if the hose is loose or damaged.
Try using some compressed air into the oil fill hole, a blow gun tip will do with a rag wrapped around the tip to seal it off. Then a cup of soapy water and a brush. Pump a little air into the engine and brush everything in the bell housing with the soapy water. If there is a leak, bubbles will tell you where it is. Give it a few tries with varying air pressure, just don't hold it wide open.
Good luck!
Tom