You basically have to re-invent the wheel. The QueryProvider is the thing that does the translation from expression trees to it's store native syntax. It's the thing that's going to handle special situations as well like string.Contains(), string.StartsWith(), and all the specialty functions that handle it. It's also going to handle metadata lookups in the various layers of your ORM (*.edml in the case of database-first or model-first Entity Framework). There are already examples and frameworks for building out SQL commands. But what you're looking for sounds like a partial solution.
Also understand that table/view metadata is required to correctly determine what is legal. The query providers are quite complex and do a lot of work for you beyond making simple expression tree conversions into SQL.
In response to your where does the second part happen. The second part happens during enumeration of the IQueryable. IQueryables are also IEnumerables and ultimately when GetEnumerator is called it in turn is going to call the query provider with the expression tree which is going to use its metadata to produce a sql command. It's not exactly what happens, but it should get the idea accross.
