There are some great you-tube videos on FMP relationships, or the FIleMaker training series, or Lynda.com, or from general web searches. Check out the relationship types, including Cartesian (the "x" relationship).
I think the answer to one of your questions, is, Yes, if you set up a relationship between table a to table b, table a still behaves the same way if you're in the table a layout, for example. Depending on the type of relationship (connection) between tables a and b would affect how values act with "sum", "count" and other functions.
So you started with files A and B, with file A having one table, table A.
You imported file B into A, so file A now has tables A and B.
Whether you related tables A and B or not, anything you do in file A in either table will have no effect on file B. FileMaker doesn't automatically add file references to imported files.
You can verify that table B on your relationship graph is coming from the correct data source (file A) by hovering over the tiny arrow in the upper left corner of the table occurrence on the graph. It should say <current file>. If it says file B, that would tell you that you're going to be modifying file B.
Why would you want to do this? What is the object of the import?