It can be difficult. At track switches, lay the straight-through cork first, then the cork for under the diverging route. Cut the cork as necessary to fit the diverging cork smooth and flush against the straight-through cork. If your track switches have holes in the centers of the ties, use these holes to set the switches over the center lines of the cork. Don't solder all your rail joints. You have to allow for expansion and contraction that goes with temperature. The key is a really sharp utility knife. Cut through the straight and diverging route cork in as a few a passes as possible. Don't worry if you loose the bevel. The most important thing is that the cork be level on both routes. You can use scrap cork to add the bevel back later.
If you really find you're not getting this right, you can order precut cork for different number switches from Walthers or get them at any well-stocked hobby shop. Sometimes this is the easiest answer to getting smooth transitions on switches.