The same way as you would do if making the entire cut with the router.
Well, one could certainly do that; however, IMO, routers are really meant to trim relatively small amounts of wood. And, IME, they work best in that manner. If one needs a bunch of 3/4 x 3/4 grooves in 6/4 oak, you could either hog out most - 11/16 x 11/16 for example - with a table saw in one pass and then make one light pass with the router to final size or you could make multiple basses with a 3/4" router bit, gradually increasing the depth. I find the former easier and better, YMMV.