Suppose that I'm a working mathematician that has just proved a Theorem, say, in Number Theory.
Does Gödel's Incompleteness Theorem imply that I can't know for sure if there exists a proof of the logical negation of my Theorem?
No, that is a complete misunderstanding (but understandable given the incorrect philosophical use often made of Gödel's theorem.
As long as Number Theory is consistent by definition there can't be a proof of the negation of your statement.
The consistency of your axiom system is something one simply has to take on faith and that has nothing to do with metamathematics. After all if the system you are using was inconsistent than any demonstration in that system (or one of equivalent power) would be useless since you can prove anything in an inconsistent system. Unfortunately, Gödel's theorems are often invoked as if it showed this simple philosophical point: if your basic principles of reasoning are flawed then you can't use them to reason your way out of the error.
What Gödel's first incompletness theorem (really the Gödel-Rosser theorem) tells you is that IF your axiom system is consistent (you can't prove any statement and it's negation), strong enough to represent basic number theory and you can enumerate what the system's axioms are (technically the axioms are computably enumerable) then there is sentence which is neither provable nor refutable from those axioms.
The reason for the confusion is that Gödel's second incompleteness theorem tells us that if a theory T satisfies the above (such as what you use to do number theory) then CON(T) is neither provable or disprovable in T where CON(T) is the formal statement that T is consistent. But a key point here is that CON(T) is undecidable in T not because of some uncertainty of the consistency of T (we are assuming T is consistent) but because it's not clear if the formal statement CON(T) really captures the informal notion of proof. Indeed $T + \lnot CON(T)$ is actually a consistent theory. It just turns out that this theory allows infinite integers which code up fake proofs for a sentence and it's negation causing CON(T) to be false even though the system is actually consistent.