Don't think the order is particularly important, but don't see how you can do both the blue and white simultaneously. You'll need to let one dry before you and tape the second. As for the paint, a decent oil-based enamel is OK. Better is a single part polyurethane like Pettit Easypoxy, and best would be a two part polyurethane like Awlgrip. I would go with the single part polyurethane.
I am assuming the current bootstripe is painted and needs renewal. On many boats (like mine) the bootstrip is colored gelcoat and just needs polishing and waxing each spring.