Couple of comments:

1) If you are building an all fiberglass boat, I think polyester resin is more than suitable. Most of the issues with polyester come from wood bonding. I have worked with both and I find no real difficulty working with poly resins. In some repects, cost, repair, finishing, I find polyester superior. Of course if you ar bonding to wood....

2) For smell, I actually find epoxy to be more irritating to me. But by all means whatever you use get some positive ventilation. If you use masks, remember the filters have pretty limited lives you will need plenty of replacements.

3) For layup schedule, a laminate's strength comes from the fiber not the resin. Personally, I would be very leery about reducing the amount of glass you are using. What is driving the decision. If it is cost, then consider going back to the poly resin. If it is wieght, you have two options: either go to different composites (different materials such as kevlar, carbon, biaxial/triaxial, s-glass, etc) which will drive up cost, Or reduce the amount of resin used. This is good practice anyway, it will reduce your cost and strengthen the layup. Doing your layups, you need to practice and work on reducing the resin ratio (squeeze it out with rollers, bagging, etc) to get maximum performance out of the laminate.