I wouldn't just cover it with a filler. That will probably pop out in due course and will definitely crack round the edges.
Start with a simple fiberglass repair kit. West Marine sell an epoxy based West Systems kit that includes everything and The Hope Depot sells a Bondo polyester based kit. As noted above, epoxy is stronger but cannot be gel coated. The boat is made of polyester and should be strong enough.
Step 1) Start off with sanding the gel coat around the damaged area away, about an inch into each direction, to make sure that the fiberglass underneath isn't damaged. If you see damage, just keep going until you are about an inch clear of the damaged area.
Step 2) Cut the damaged fiberglass away while trying to keep the foam layer intact with a Dremel. The fiberglass layer isn't more than a few mm thick. Clean the area with acetone.
Step 3) If the foam is soft, inject resin through the foam to bond the foam with the inner layer of fiberglass.
Step 4) cut out pieces of fiberglass in the size and shape of the damaged area. Depending on the thickness of the glass fabric, you may need quite a few layers.
Step 5) mix the catalyst with the resin and stir thoroughly. Make sure you wear disposable gloves!
Step 6) use a small brush to 'glue' the pieces of fiberglass cloth to the foam. Keep adding layers until it's flush with the area around the damage.
Step 7) add 3 more overlapping layers on top, the largest layer should cover the sanded area around the damage.
Step

mix a fairing component with the resin until you get a peanut butter-like consistency and apply this to the damaged area until the fiberglass texture is no longer visible. Let it cure for 48 hours.
Step 9) lightly sand any imperfections away
Step 10) paint or gelcoat the fiberglass.
Check out
http://boatworkstoday.com/. Andy has a couple of great step by step videos for doing similar repairs.