Set the bit height so that the tongue or groove (depending on which bit you're using) is at the desired height (probably centered on your stock). Cut the profile as you normally would (I'm assuming you're using a router table, which is the only way I've used a T&G bit set). Then you can use any good mortising bit of the correct diameter to remove any material remaining that would interfere with the joint. From the tongued boards it is very simple, just remove the small lip of wood above and below the tongue. The grooved boards is more tricky, but using the tongued boards as a guide should allow you to set the bit height just right (this is how I did it). It's not the most elegant approach, but it worked.
Now that I have a Unisaw and a very good stacked dado set, that's the way I make T & G joints now. It is much easier and more straightforward than using the router set, IMO.
Mike