Hi Cactushead. It's not so bad...
Go to the advanced tools part of the track pullout, where you apply heights, and add spline points. In between the add and adjust spline points and where you can apply and get heights is the section for applying grades.
There are probably right ways, wrong ways, and easy/easier ways of doing things, but here's my way so hopefully it works for you.
I lay my track where I want it to go regardless of how high it's supposed to be. I then set the height on the first point and then get the height on the last point. This gives me a reference to start from, like nailing a piece of string or wires down on a table. I then use the get gradient of the tracks. Sadly, this is for each segment between each spline point and not for the whole length.
Now here's a bit of a tricky thing. First of all, never apply the gradient or get gradient from the spline points. Instead get and apply gradient to the track only. So I now have checked the height of the second point off the starting point and adjust upwards. I then check the gradient, of the track only, and if it's realistic, i.e. under or about 1%, I'll leave it and continue on to the next point and repeat until the track is smooth. Once that's done, I then check the track overall for any dips and twists. Sometimes, there are going to be cases where the grade has to be higher than 1% and there is no way around them. In these cases, I try not to make them ridiculously steep, otherwise, the line becomes like the New York EL as it goes from the bridges to the tunnels.
I will say that doing this on an imported TransDEM map is actually easier. I simply set the heights at various points on the stretch of track and then let the grade smooth out in between. For the most part, this is pretty accurate and very close to the actual route.
There is one thing to keep in mind. The grade will be steeper with curves, which I don't understand why, but this is the case so you may have to do additional adjustments and take this into account when planning the grade.
I hope I explained this okay...
John