So you're using TRS2006. I use that too, and downloading can be a little bit of a pill sometimes. CMP (Content Manager Plus) has a tendency to glitch often. But, first off, where did you find the nycta2007's, because I'm not finding them on the DLS (Download Station).
To make a route go to surveyor from the main menu and down at the bottom there should be an button that says "Create New." Click that and you'll see a baseboard map that is just a grid. Set the specifications for the route you want to build, such as what measuring system to use and the name of the railroad. I'd suggest, since this is your first time, to just have fun and make a new route. Download some other routes from the DLS and see what people have done. Don't expect it to be right your first try. I'm far past my first try and my routes are still not perfect. It's a total "beaver's dam" type experience with route building. Anyways, I digress, you'll see a sidebar on the right of the screen. The top bar is your terrain tools, allowing you to place water (at specific heights) change the landscape, etc. The second tab is the terrain texture tab, so you can paint the ground. It's easier to shape the terrain when you see it as a grid. You get a better depth perception in my opinion. The third tab is your objects tab, which ranges from anything to common buildings, trees, animals, industries, people, static vehicles, and spline objects such as fences and walls. (To get spline objects click on the second button at the top of the object's menu). The fourth tab is your track tab. You can place any track you have or have downloaded, which is highly recomended. There are a lot of track types out there that aren't immediately available at the start, such as monorail track, 30" gauge track, 42" gauge track, and plenty of others. The fifth tab is the tools tab, which has a couple of functions. You can place rulers to measure distance, turn radius, etc. You cna also place cameras so that, when you're in driver mode, you can view the trains in a cinematic mode. You can also copy and paste terrain, terrain textures, and objects. The sixth tab is the world tab, which allows you to see the railroad in different weathers, times of the day, change the sky-type (cloudy, clear, etc) and change the water type (rough, calm). The final tab is the trains tab. You can choose any engine from the list, whether you've had them from the start or downloaded them, and place them on the track, even regardless of the gauge of the track. You have a wide variety of engines and rolling stock to place, so have fun.
I hope this helped. Have fun with Trainz.