>if anyone had any ideas for how to keep the grove for the wheels as best as possible?
Put a piece of thin card or plasticard hard against the inside of the running rail until the polyfilla has dried? You may need to coat the outside of the card with something to prevent the polyfilla sticking - maybe sticky tape?
You will need to be sure that the polyfilla in the centre is no wider than the minimum back to back wheel measurement of the locos and wagons you are running.
David