No. You need underwater filler or epoxy. Plastic Padding do underwater in tubes for small jobs, but if you are doing a lot then probably worth using something like International Watertite or mixing your own using epoxy and a fairing filler.
If it's just dings and scrapes in the gelcoat then you'd be better off filling it with gelcoat or an epoxy filler which will have far superior adhesion than the Isopon which will be based on a cheap polyester resin. If you really need it to be fast and dirty then the Isopon will be the cheapest.
White superfine Milliput does me for covering over screw heads in gelcoat and for minor dinks. It doesn't quite match the gelcoat but then neither does the gel filler. It lasts indefinitely on the boat and is very easy to use in small quantities. A definite place in the 'repair materials' drawer.