I working on a project like you do. I'm using Database First Approach. After create a project with Individual User Authentication, you need to transfer these user tables to your database. You can do this with schema compare.
On the SQL Server Object Explorer > find your localdb that contain user tables > right click > Schema Compare
schema compare
Then select target (your database) and click Compare on right corner.
Select table(s) you want to transfer to your database.
After doing this edit Web.config file:
<add name="DefaultConnection" connectionString="Data Source=YourServerName;Initial Catalog=YourDatabaseName;Integrated Security=True" providerName="System.Data.SqlClient" />
(This connectionString is to use default model, controllers and actions provided by project. If you want to create your own functions for user operations you only need to add below line after transfer tables.)
Here, provider name is important. Don't chance it. This connection string is for user operations.
Then add ADO.NET Entity Data Model to use your other tables with Entity framework
<add name="YourEntityName" connectionString="metadata=res://*/Models.Model1.csdl|res://*/Models.Model1.ssdl|res://*/Models.Model1.msl;provider=System.Data.SqlClient;provider connection string="data source=YourServerNameL;initial catalog=YourDBName;integrated security=True;multipleactiveresultsets=True;application name=EntityFramework"" providerName="System.Data.EntityClient" />
providerName is important here as well.