If you use "aye", you would need to adopt the other conventions that go with it (eg. using "nay" for "no", etc). It wouldn't work as a substitute by itself.
For example:
Q: "Are you managing work OK?"
A: "Aye, I'm managing it very well, thankyou." --> Too strange! "Aye" is out-of-place here, against the regular polite English.
A better (pirate!) answer is: "Aye, that I be. 'Tis a task safe within me humble abilities, thankin' ye."
Don't forget the accent. ;)