If you already have a specific tolerance group, in the following transaction you are able to assign it to specific user. If a user does not have specific assignment here, it is assigned to the global tolerance group for a particular company code.
IMG Path: Financial Accounting (New) -> Financial Accounting Global Settings (New) -> Document -> Tolerance Groups -> Assign User/Tolerance Groups
When you enter into the transaction, you could either change existing assignments or create new entry.
On following screen you could see the assignment. Fill a user id and a tolerance group and hit “Save”.