Since I can't tell by looking at your post if you have registered, I had to ask, not only for legit reasons but because the answers can be different depending on the version.
Asking the the same question in different messages is also generally frowned upon unless you have a related followup question that deserves its own thread. See
here.
As a rule, if any object shows errors in CM, it will appear in red text in Trainz and won't be selectable to place in Surveyor.
In CM, right click on the object and pick show errors and warnings. Each one needs to be fixed and depending on what they are, it can be a quick easy fix or a long complicated fix. You will have to copy and post the errors to get any help in that regard.
Since TRS2009 didn't have layers, adding and removing train objects is as simple as opening the train tab, selecting a new vehicle, highlighting the add button and clicking on an empty section of track that is long enough to accept it. You remove a vehicle by highlighting the remove button and then clicking on the vehicle, it will disappear from the track.
Changing the color of a vehicle involves opening it for edit by Explorer in CM, modifying the relevant texture files, closing the Explorer window and committing the modified asset. If you did everything correctly, the object will have a new color scheme. This is not for the faint of heart and requires a solid knowledge of how textures are applied so that you can modify them with some reasonable expectation of getting your desired results. As a rule, make a clone of the object before you attempt any modifications. That way if things don't work out, you can always start over with a fresh copy.
Modifying the shape requires you to have the original mesh files. Few content creators will release these so this is not something you will likely be doing unless you make your own objects. Then you can change them to your heart's content. By the time you get to this stage, you will know how to do this.