When you choose the link option on source tables that are not linked to anywhere, you are going to affect those tables in the other database assuming you have permissions on the location of the source db. If you import the tables, you have independent copies of them if the source tables are not linked, and if different people are using both of these db's the records will likely differ between them. However, if the tables are linked in the source db (the one you're copying from) your copied tables are linked back to the original source, just like the ones you copied from are, because you cannot import tables from a database as physical tables if those tables are linked - you can only import them as linked tables.
Let us know when you've had a chance to perform my previously suggested steps (I presume that's what you're up to next).