Kanazawa to Nikko by train

What's the cheapest route? And which is the best site to find it.

the only one i found was hyperpedia and its not a cheap route at all going the long way around via osaka.

Is it possible to take a more direct route but buying tickets along the way or something or making train connections? So long as it doesn't take me more htan one day travelling, i wouldn't mind too much changing trains so long as i don't have a high risk of missing a connection.

Any ideas on this?

What's the cheapest route?

Train is rarely the cheapest. An overnight bus from Kanazawa to Tokyo followed by a Tobu Railway ride to Nikko would likely be cheapest.

Tokyo-Kanazawa bus:
http://willerexpress.com/

If by train, then taking local trains all the way would be cheapest, but the trip would take an entire day and still be more expensive than the bus.

And which is the best site to find it.
the only one i found was hyperpedia and its not a cheap route at all going the long way around via osaka.

Hyperdia is the best site. Under "Search Details", uncheck all the fast train types (basically everything but local trains) in order to get the cheapest connections.

Note that the travel situation between Tokyo and Kanazawa will change drastically on March 14, and online timetables don't handle dates after that date yet. In particular, some trains along the cheapest connection between Kanazawa and Nikko will turn non-JR and become a little bit more expensive.

Is it possible to take a more direct route but buying tickets along the way or something or making train connections?

If you take local trains, you will have to change trains many times along the way. The more tickets you buy, the more expensive it will become. The cheapest is to buy one ticket all the way for each railway company used (e.g. JR or Tobu). Long-distance tickets will be valid over multiple days and allow for getting on and off along the way (but no backtracking).