Do you spar? As long as you're not constantly getting out muscled by guys the same weight as you, you should be fine. You just need to box and not try to brawl with guys who are stronger than you.
Ectomorphs are perfect for boxing. In the amatuers the scoring favours tall thin guys who have the best reach in their weight class. As a short guy I'll give you this piece of advice though, as long as you get good at moving and don't 'bring it' to the short strong guys you'll probably outpoint them.
Learn to hit hard. Being a skinny guy who can hit like a mother****er is great for frustrating/keeping people off you when you want, so you can slow the fight down and go at your own range/pace. Throw in combos, and hit the body. Long arms are great for sneaking in a hard body shot at mid-range. Head-body, body-head. Keep them guessing. You can pretty much reach them with anything, so you have a lot of options for stringing combos together. Work, work, work on your jab. Make that punch amazing. Nothing worse than a guy who can control you with his jab when you can't even get to him.