Answer by Professional Japanese Teacher
You are right to say that the word “soo desu ne” means agreeing to what you’ve said. However, it is also used to indicate that the listener has understood what you have said. He may or may not agree with you at the end.
In your case, your boss indicated that he understood your proposal but maybe the proposal needs further consideration. If he agrees to what you have suggested, he will give a definite answer such as “じゃ、そうしましょう ja, soo shimashoo” (let’s do it).
Sometimes, Japanese expressions can be a bit ambiguous so you have to listen right to the end before making judgements.