In my opinion EF is better than Linq to SQL. Like anything it can be used well or poorly. I prefer to use stored procedures because I believe they make maintaining and tuning the T-SQL much easier. You can use SP's with either EF or Linq to SQL, so you can do it. I think Florian Reischl has a good series on his blog about business layers, data layers, and database access, starting here, http://florianreischl.blogspot.com/2011/09/tables-are-no-domain-objects-part-1.html

SQL Server MVP Mladen Pradjic also has a good post about this here, http://tinyurl.com/DecouplingPrajdic