If you mean that you have a table which relates to two other tables:
Products:
ID
Description
InStock
Customers:
ID
Name
Address
Orders:
ID
CustID
ProdID
And "Orders" is your "Junction table" then yes, you do have to insert values to that yourself - the system doesn't have any idea what customers bought what product!
If that isn't what you mean, you are going to have to be a lot more specific in your question!