if you can only have one autonumber per table
First off I fear you misunderstand the autonumber, primary keys and foreign keys.
1. The autonumber can only be used once in a table, you are correct. But a table does not need more than one autonumber. The autonumber is used as a surrogate key and if set as the primary it has it so that the same number can't be used there more than one time.
2. When you have other tables you want to link to them, your other tables probably will have an autonumber primary key as well. HOWEVER, you do NOT link those to the other tables. The other tables would have a FOREIGN KEY which is basically the same field as the parent table but as a Long Integer. See this sample:
table -
Employees
EmployeeID - Autonumber (PK)
FirstName
LastName
table -
Departments
DepartmentID - Autonumber (PK)
DepartmentName
table -
EmployeeDepartments (a junction table)
EmployeeDepartmentID - Autonumber (PK)
EmployeeID - Long Integer (FK) - the autonumber from the Employees table
DepartmentID - Long Integer (FK) - the autonumber from the Departments table
So see how they are used in the tables? Then you have your links for the forms - the main form here in my example would be the Employees and then it would have a subform consisting of the EmployeeDepartments table and the link would be
MASTER - EmployeeID
CHILD - EmployeeID
And we don't even include the Departments table in that because it is a completely and separate entity.