Here are the sentences, "We have been working for three hours." Or "We have been working since three o'clock." Does "twazè or Twa zè" means three o'clock? Does "Twazè tan or Twa zè tan" means three hours or the reverse?

It's "twazè"  → 3 o'clock.
It's "twazèdtan" → three hours

"We have been working for three hours."
"N'ap travay depi twazèdtan."

"We've been working since three o'clock."
"N'ap travay depi twazè"

See the four posts on telling time link

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