Please advise on what is best route to get from Milan train Centrale to Duomo plaza
And then from last supper back to train station.
It takes about 15 - 30 minutes by cab to get each way (very much depends on traffic), walking about half an hour. Not sure what you mean by route, like specific directions? For that, definitely download the map of the area you want to your phone so you can consult it offline on Google Maps.
Is there a subway from Milan Centrale to Duomo.?
I took the metro from the train station to the Duomo and a tram from the Duomo to the Last Supper sight. I believe there's also a metro from near the Last Supper back to the train station. I don't recall specific metro/tram numbers, but that information is detailed in Rick's guidebooks. If you haven't already done so, you should buy a guidebook for your trip.
Take the green line from Milano Centrale to Cadorna, and from there it's a 7 minute walk to the Last Supper.