It is easy to go by your own. Hangzhou West Bus Station have direct shuttle buses to Huangshan Scenic Area (Tangkou), not Tunxi (downtown of Huangshan City). One night there is enough. Take early bus from hangzhou, then you have more time there. You mean the cost of the tour to the two villages? You may inquiry some traven agent. The cost include your hotel in Huangshan. If you want to see the two villages, I suggest you to stay another night. The transportation to them may not easy for you. If you can not find the bus station, just rent a taxi or van, not cheap but convenient. You can get back to Tunxi from Tangkou first. I think about 400RMB is enough to hire a car from Tunxi-Xidi-Hongcun-Tunxi.

Hi ms Cindy, thanks for your advice if I were to only go to one village, will 2 days 1 night be enough? How should I leave huangshan for shanghai if I wan to stay one night, see the village and have a day in shanghai to spend? Thanks!

Actually no much difference whether you'll visit one or two villages, coz the villages are not far from each other. If you really want to go, just squeeze some time from your huangshan tour and hire a car to save time. But time is very tight.
There is direct bus to shanghai from both the huangshan scenic area(Tangkou Bus station) or the downtown area (Tunxi Bus station).
If you'll visit the villages, no need to go back to the scenic area, you can take the bus at Tunxi Bus station.