Sounds like a one-to-one relationship. Table A queries Table B and Table B queries Table A?
I prefer using the relationship design tool in Access because it enforces referential integrity. However, using a query to relate to another table would work -- Access is fairly easy to use, and this approach may seem logical to someone who is not familiar with proper desgin. This approach is more often used in the form.
Also sounds like a bad or suspect design. I do not use 1:1 relationships much except for security where one table has the "public" information and the second table has the "private" information. For example, HR public info for an "employee" table would have fields for their name, address, title, etc. The HR private info would have fields for current salary, medical note, etc.
Another place to use this would be a manager / employee info where an employee has a manager field pointing to another employee in the same table, but I digress.
If the application still works, then you may want to leave it as it is. Changing the schema when their is a lot of data can be fairly high risk and take a lot of work.
If you decide to design the DB then supplying a little more specific info would help envisiion the problem.