Discarding is a normal practice in most fisheries. If you do not enter any information, you are assuming that discarding does not take place. If discarding does take place this is worse than guessing! Therefore, it is better to use information from similar fisheries in other areas or perhaps based on interviews with fishers in your area.
Discarding may affect trophic and population dynamics. For example, in shrimp fisheries where the discards include predators on shrimps that may be turned into food for shrimps, a trophic ecosystem model can be used to quantify the role of discarding. Note that you must tell Ecopath where to send discards using the Discard fate form.