Once your seed is loaded into the tracker, each location will start with a question mark next to it.
As you find Ansem Reports in the game, each report will tell you how many Important Checks are in a specific location, and a number will replace the question mark in that location.
Hint logic dictates which locations must be hinted based on where proofs are located. The hint logic is detailed here.
What are “hinted hints”? Why do they matter?
(Taken from the hint logic page linked above, but also included here for additional emphasis)
Reports pointing to proofs will be hinted. As an example:
There’s a proof in Port Royal. Report 4 points to Port Royal. Report 4 is in Halloween Town. Halloween Town must be hinted by another report. If the priority items above (proofs, forms, pages, and magic) are already taking up all 13 hints, they will be prioritized over these reports. Note: If the reports are on drive forms or in 100 Acre Wood, there is no logic to hint forms or pages as of now.
A “hinted hint” is represented in the tracker by the location’s number turning a different color (by default, yellow).
In the screenshot above, Ansem Report 9 (found in Pride Lands) hints Halloween Town. Halloween Town gets a white number because Pride Lands has not been hinted (yet). Ansem Report 11 hints Beast’s Castle. Because there is already a hint pointing to Halloween Town (where Ansem Report 11 is located), Ansem Report 11 becomes a “hinted hint” which turns the number for Beast’s Castle the hinted hint color.
Based on this information, it could be inferred that Beast’s Castle may have a slightly higher chance of having a proof than Halloween Town would, since its hint is hinted. HOWEVER, being a hinted hint location does not guarantee a proof. Only once all 13 Ansem Reports are found is it guaranteed that a proof will be in a location pointed to by a hinted hint.
A general rule of thumb is to not get too caught up in hinted hints early in a seed, unless using them as a tiebreaker in an otherwise 50/50 decision of where to go next. As you get closer to having all 13 Ansem Reports, the more likely it becomes that a location pointed to by a hinted hint has a proof.