1. Never let the vertex handles cross over the track, unless it's for intentionally putting a bump there.
2. Try using vertexes that are about the same distance apart. It will make it a lot easier.
3. In general, make the length of the vertex handles proportional to the length of the track segment they define. (I.E., if there is a shorter segment followed by a longer one, the vertex should likewise have a short backwards handle versus a longer forward handle.
4. Try to use at least one vertex for each 90 degrees of lateral turning or 90 degrees in change of vertical angle.
5. Make sure that you are either turning at a constant radius, or that the radius is constantly decreasing or increasing. Don't go back and forth.
6. (two interesting methods)
6A: (for small bumps only) Run the track through the AHG with 0 heartline and a vertex every 8-10 m or so, and and it will very often take care of small bumps.
6B: use the "split up" feature to divide the segments before and after a troublesome vertex. After using the smooth feature, delete the middle vertex, split up the resulting long middle segment, re-smooth, and then delete the two vertexes that you created at the beginning. This will very often lead to smoother vertexes.