I’m not too sure I understand the problem, but it seems to either relate to layers (which I know nothing about), or the difficulty in picking up assets or splines in areas where they are closely grouped.
If it’s a layers problem, there is a lot of discussion in a parallel thread here.
If it’s closely grouped items then here are some methods you can try:
1. Always try to work from directly overhead to grab the item. It is easier to pick up the correct asset from that position.
2. Clicking the right mouse button (RMB), when directly over the asset, will light it up briefly, acting like a torch to show it up better on the baseboard. That trick is particularly useful if the baseboard is textured in a similar colour. Billboard items can be particularly difficult to see from directly overhead, but show up, momentarily, quite well using this “torch” method.
3. When you have grabbed the asset using the left mouse button (LMB), keep it pressed as you move it to its new position. The same system applies both for moving laterally, or changing height.
4. To get a better view, keep that LMB pressed, but use the up/down/left/right keys at the same time to get your preferred angle for final placing. With practice, you can also roll the mouse wheel with your second finger. That way you can fly around all over the place without losing the asset, as long as you keep that LMB pressed. When you have selected your final chosen position, release the LMB.
5. Some splines can be difficult to place if close to other spline points, when Trainz often won’t let you release it to where you want it to go. When that happens, place the spline end a short distance away from where you want it, making sure it is in an open area. Then use the move button, pick it up again and place it exactly where you want it to go. Use the Shift key if you want to avoid it snapping to another spline point.
This works for me in TRS2004 Surveyor.
I can’t say if it will work in other versions (or Mars).
I'm guessing it will though!
I hope this is helpful.
Cheers
Casper