How do I mate two 2x6s together to make a 4x6 beam?
Keep in mind that lumber nominal dimensions are not actual dimensions.  A 2x6 is really 1.5" x 5.5" not 2" x 6" as the name suggests.  So a built-up beam made from two 2x6's is actually just 3 inches wide.  If you're supposed to use a 4x6 timber, you might not be able to substitute a built-up beam made from two 2x6's.   

Using built-up beams made from doubled up or tripled up dimensional lumber is an everyday framing method.  The most common way to build them is simply nailing them together.  There are different standards for the specifics of nailing them up. 

This illustration from Details for Conventional Wood Frame Construction shows nails 32" apart in a W pattern, with three nails at the ends.  The document specifies 20d nails.  Other standards may specify different types of nails and spacing.  



It may not seem like a lot of nails, and there's no glue, but it's not necessarily better to make the beam more rigid;  this type of beam may function better if the pieces are allowed to move a little so that all the pieces contact the material they support.  The important thing is to stick to whatever the design intended, and that that design is something applicable codes allow.