The ttdpatch was created by Joseph Drexler and Marcin Grzegorczyk. The only way to play ttd on windows xp and windows 2000 is through the use of the patch, so it's been a life-saver for many ttd players who couldn't play because of their os (operating system). The ttdpatch site has it's own manual but was a little hard to understand to the new ttdpatch players. Seeing as the patchdudes didn't have enough time to write a tutorial, I decided to give it a try.

Pre-signals can be very confusing at first, but once you have learnt to use them they're very helpful. Pre-Signals are used mainly for stations, what a pre-signal does is "signal red" when the two (or more) signals in front of them are red. It eliminates the need for a "passing loop" when the station (or whatever) is used.
Building Pre-Signals is very easy because most of the times the signals will be automatically built/upgraded when needed. Firstly build the station (I'll be using the station for an example) normally.

Build your station which ever way you prefer and remember to put the "two-way" signals at the entrance of the platforms. Once a train passes the first signal, the signals will automatically upgrade.
Note: you can also change the signals manually by holding ctrl while building the signals.

The red circle shows the "entrance" to the pre-signal area, while the blue shows the "exit" to the pre-signal area. The entrance signal will be red if the two exit signals are red (If the two station platforms are occupied in other words). This setup will only work if there are two or more exit signals, other wise the entrance signal will be red forever.

If you've already tryed some manual pre-signaling yourself you may have noticed the "combined" pre-signals. These are pre-signals which are both entrance and exit signals.

As you can see the one of the combined signals is red and the red train will be forced to take the second route. Using this method you can have two trains enter the station at simultaneously.
Note: The combined signals can only be made manually, if you build this setup using normal signals it will not change automatically.

Most people new to the ttdpatch mistakenly use this switch... It unloads the cargo onto the station (so it's "en-route") no matter what, even if that station accepts the cargo. So most people new to the ttdpatch mistakenly set their trains to unload. This leads to many new topics on the forums "Station doesn't accept cargo" etc. The main reason I put this in the tutorial was to tell people of this fact.

Back before the patch came out when you used two (or more) vehicles (eg. a ship then a train) to transport material/goods to a station, only the "last" vehicle (the vehicle to deliver to the factory/whatever) will get paid. This is where the feeder service comes in, it divides the income made over all the vehicles used in the transporting process. This is vital, especially if you want a good performance rating. As one of the requirements is that all vehicles (over 2 years old) make a profit of over 10,000 pounds (20,000 dollars). The feeder service is easy to use and learn, I'll use an oil rig as an example.

The oil is picked up at the oilfield and delviered at the dock/train station (remember to put "unload" in the ships orders). Once at the station the oil is picked up by the train and delivered to the oil refinery. This is an excellent way to transport oil from the rigs early in the game, when it'd be too expensive to build a train line to the rig and you feel ships are too slow.

The income gets spread evenly across the vehicles. You can see the route would be too large for a ship to travel without losing considerable profits, so the use of the feeder service is more profitable.

Waypoints are needed for more complex train networks, where it is easy for a train to get lost. A waypoint is usually a 1x1 station which is placed on the track in which the train needs to take. Waypoints can also be used for stations, "spliting" them up into 2 parts "pickup" and "delivery". To use a waypoint correctly, you add it to the trains orders with " non-stop" command. This causes the train to pass through it but not stop at it.

This is a screenshot of the network used in this (waypoints) example. If waypoints were not used the 4 (out of 6) trains would get stuck at the Wrinningbury North station, mistakenly thinking it the way to their stations.