Frankly, your best cheapest bet is to buy a gelcoat touch up kit and repair the scratches. Some ski manufacturers sell them with the exact color. If not, you can buy a generic kit and mix the color yourself. It won't be perfect but will likely look better than a crappy paint job. I did this multiple times on my sailboat and it is really pretty easy.
I would never recommend painting a boat with spray can paint. It is way to hard to control the amount of paint applied so you will get many runs. In the past, I had one of those electric household guns, and my success with it was mediocre. Others may have faired better than I.
If money is no object, find somebody with a good automotive air system and have them do it. Sometimes you can get body shop workers to do it on the side.
If you don't want to spend that much money and don't mind putting in some effort, I would suggest that you paint it using the "roll and tip" method. (Look up on YouTube). I have used this technique on the sailboat and two of the kayaks that I built and the results are almost as good as gelcoat. To do it right takes time and the biggest key is surface prep. Generally speaking, you first have to clean the surface removing chemical contaminants. Things like the "speed juice" that some apply to their hulls or some errant bug spray will ruin a paint job. Sanding does not remove that stuff, it just smears it around. Next you will fill any holes and rough up the surface with sand paper. Most paints will provide very specific directions regarding how to overcoat gelcoat. You may have to call their customer support line to get the info. You will likely need a coat of primer then at least two coats of paint, wet sanding in between each coat. White paint over bright colored gelcoat will take more coats or the color will show through.
I strongly recommend that you stick with a high grade marine paint like Interlux or Epifanes. Mono-urethane paint is harder than enamel but is less forgiving to apply and requires more coats.
Multiple colors are easy but you have to be meticulous with your masking. On the edges, that blue tape is not good enough and will leave a rough line. Use 3M Fine Line tape instead.
The link below has a pict of the sailing skiff that I just completed. I applied 3 coats Epifanes Mono over one coat of primer using roll and tip. (Sorry that I have not figured out how to embed pictures)
Goat Island Skiff