SCTweak allows you to manually add overpasses (bridges) and tunnels to your city. I was able to play around with this modification for a bit to see how it works, and it worked the way I imagined it would. I do have a few complaints, but I still think the mod is worth the download! It doesn’t use the road guides the way I would like it to, and it isn’t really friendly with the curved and curvy road tools. Other than those small complaints, I highly suggest you check it out if you’re interested in placing bridges and tunnels in your city where you want.
The modification doesn’t require you to modify game files, rather it works as a separate piece of software that runs in the background.
Please note: Maxis doesn’t fully support modifications as of yet, so install and use them at your own risk!
Check out this video to get an idea of how it works: