1280 yen one way if you use a local train between Shiojiri and Nagiso or around 3000 yen one way if you use a limited express train.And do I top up at the train station prior to the journey or at the end of journey?
If you use a local train, you can do when leaving Nagiso Station (or to a conductor inside the local train if one passes). If you use a limited express, you can buy it on board of the train when using unreserved seats, but you would have to buy it in advance if you want to use reserved seats. I recommend to buy it in advance. Basically, you need a ticket for the section between Shiojiri and Nagiso.
Also, is there a website where I can check to extra train fare one need to pay if the journey is not fully covered by the JR East Pass?
Only with a knowledge of the train network:
http://www.jorudan.co.jp/english/norikae/
