I am planing a trip where I go from Tokyo to Sapporo and back using the Hokkaido and Higashinihon Pass. On the way up I want to go strait from Tokyo to Sapporo. The website has a example time table showing that it is possible (http://www.japan-guide.com/e/e2362_03.html). I however cannot find what train lines it used or any other information saying how to get there.

Does anyone know the specifics? ex: take ABC line from Ueno to Station A then transfer to the DEF line and so forth.

As mentioned in many other threads check this website for routes available for the dates and times of your trip:

It is not possible with the Hokkaido-Higashinihon Pass. Due to bad train connection, I think it can barely be done in 2 days.

I'd like to stop in Hakodate on the way back.

Then you might need three days when using the Hokkaido-Higashinihon Pass.

I'd rather try get back in a day like the way I get there.