Hi Patchy,
If you have Trs2006, I recommend that you use the hole punches, tunnel mouths, wing walls, grass planes and tunnel bores which are included objects and splines. You can find them used on the Hawes Junction layout.
Although you need to practice to use them correctly they do allow the tunnel mouths to be located anywhere and at any angle.
If you have TC3 you can also alter the pitch of the tunnel mouths to accommodate gradients.