Sounds like you used Marine-Tex or another similar product. Your repair method is one that many Hobie sailors take, but unfortunately it's a poor shortcut for a proper repair.
Your putty job may look good for a while, but know that this is not the way to make a structurally sound, long lasting repair. The putty you used (epoxy or otherwise) is simply not equivalent in strength to the original fiberglass/foam sandwich hull construction. Epoxy putty has high compressive and shear strength, but nowhere near the tensile strength of fiberglass cloth. As a result, it will eventually crack out due to the flexing that occurs in a Hobie hull. Depending on where the damage is located, that may happen the first time you sail the boat, or it may not happen for years. Just know that eventually, it will happen. Once the putty begins to crack, it will allow water to seep into the damaged area and into the foam core. When the foam core is continually exposed to water, it will break down and the hull will begin to delaminate in that area. You'll have a bigger job on your hands.
The proper way to fix the hull- a method that will last the life of the boat- is to grind out the damaged outer fiberglass skin and remove any damaged foam core. Then repair any damage to the internal skin, bond in a new piece of foam core material, and then laminate new glass to the outside surface. Finally, gelcoat the repair.
Using epoxy on an outside surface of the hull is also a big no-no if you ever want to match the gelcoat and have a cosmetically finished repair.