Do you want fudgy cookies or crisp? For fudgy melt a couple oz of chocolate than add the creamed butter and sugar (don't let the butter completely melt - just a couple quick stirs) then add your flour (kinda like making brownies, add cocoa to the flour tooo if you want a more complex richer flavour). For Crisp definately do the substitution of cocoa for flour.
I make two versions of choc choc chip, both of which add cooled melted chocolate to the dough after creaming butter with sugars.
One is not very rich -- if making a standard batch of dough (with 2 sticks of butter) add 2 oz cooled melted unsweetened choc.
The other is very rich, nice and chewy, from Tish Boyle's cookie book (her version uses white choc. chunks instead of semisweet chips.) She melts 3 oz unsweetened cho. with 2 oz semisweet. She also adds 1/2 cup cocoa and interestingly 1 tbsp of molasses, which adds some depth, but can be omitted with no problem.