Layout design and operation
Think about how you want your trains to run
How many operators will you have?
Where will trains stop (and, importantly, where will they not stop)?
How many trains will run at any one time?
Do you want automatic operation, or a combination of automatic and manual operation?
Will your layout have bi-directional running on specific track sections?
Consider train lengths; it is advisable to plan your block (or track section) lengths to be able to accommodate your longest train
At the risk of stating the obvious, a layout will always work best when its component are clean and well-maintained. This includes, track, engines and unpowered roiling stock.
Ensure track is well laid and kept clean
Ensure your locomotives are running well, and have sufficient electrical pick-ups
Keep your other rolling stock in good order; make sure couplings are reliable, and consider adding electrical resistors to wheel sets (this enables the computer software to sense (via current draw detection) that stock is still in a particular section of track even when the locomotive has left it)