Your SqlDataProvider is what will be used to setup the database structure for your module, so it needs to contain the most up to date scripts.  If you have renamed or created stored procedures, you will need to make sure that your script is creating those correctly.

The .dnn file will map user controls to a module control in DNN.  All of your user controls that you are loading through DNN will need to be represented in the <controls> element.  The resource files and user controls also need to be represented as files so that they are placed in the correct location.  There are two options for doing this.  You can create a zipped resource file that contains all of your user controls and resource files in the correct structure, and then set that file in the <resourcefile> element (before the <modules> element).  If you aren't using a resource file, every file that you want to end up on the user's site will need to be represented in the <files> element.

Hope it helps!

DeVen wrote If I changed the default name assigned to stored procedure, create other stored procedure, or add a user control or a resource file, have I to modify .dnn file and 01.00.00.SqlDataProvider file of my module before packaging it?

You need to modify the SqlDataProvider file to include all database modifications to be made and you need to adopt the data access code to use proper objects.

For universal usage, replace default [dbo]. with {databaseOwner} and precede all object names with objectQualifier (that's why the objectQualifier in development.config is set to "dnn_", to leverage this task).