I'm trying to say 'Although you are small you can accomplish big things" , Does 'kwake' sound right for 'although'? thanks!

Yes, it does.
although → kwake, byenke, malgre

Although you are small, you can accomplish big things.
Kwake ou piti, ou kapab akonpli gran bagay.

Haitian Creole ↔ English Reference, Look up Haitian Creole and English Words