You can use track marks and direction markers.
Track marks will guide the drivers through complex junctions and areas.
Direction markers are like one-way signs. You point them in the direction you want the drivers to go. If the driver encounters the point-end of the direction marker, they will not, or should not, go in that direction.
As time goes on, you'll gain more experience and begin to anticipate what the "AI" will do. In the process, you'll also come up with some interesting swear words and lots of creative names for AI drivers. You'll also blame the AI drivers for drinking more than tea, soda, and coffee at lunch and end up firing them all. ;-)
Anyway...
Navigate to... means that the AI will find the quickest way between points and will do what they have to in order to get to their destination.
Drive to... is more specific and is used for those places where you want the AI to head to a specific location using specific tracks. In either case, the AI will still complain about the route not being available if it's blocked.
Here's a couple of tips regarding track marks.
When you have a yard or sidings, the AI will take the shortest path between two points. This means they will take the junction and 99.9999% go through the yard rather than stick to the 65-mph bypass line. To prevent this, place some navigate to track marks in the middle of the bypass track. By placing the markers in the middle of the bypass track, this will get the AI away from the yard lead. I go one step further. I will place three sets of markers. The first is just past the junctions, the second is in the middle, and the last are farthest away.
If you use wyes, place a track mark on each point and in the middle of each leg. From my experience, AI will do a weird reverse move sometimes to turn their train around on the wye. To prevent that, again to get them past the junctions, I direct them to the middle of the legs. This keeps them on the route they're supposed to go and prevents the absurd backup, reverse, forward move.
Signaling will be another bag of worms to deal with. Unfortunately, I can't help you with German signaling with this route but later on if you bring up a post on American signals, I can help you with those.
You may be implementing the Load command incorrectly. For the most part, using the Navigate to... Industry/Station - pull down the field and put in industry/station, followed by the Load command works pretty well. The AI will slow down when the station script "grabs" control from the AI and stops the train at the platform. Once the script finishes, the AI will pick up the next command in the queue and continue on to their next destination. This is the backbone of most operations and whole schedules can be built around this for passenger and even freight operations.