get your JR pass first if u gonna take a lot of trains. go to JTB their taka retail... take the brochures there to take references.
Please DO NOT do this unless you are absolutely sure that the JR pass will cover your trips fully. Check hyperdia for the fares of the routes that you are taking first. Obviously you will need a rough itinerary before you can check. So please, draft an itinerary first before thinking about anything else.
JR pass can wait. The JR pass exchange voucher only has a 3 mth validity anyway. And I've never heard of JR pass "running out" or OOS. There's is NO hurry to get a pass when one doesn't even have the itinerary yet.
TBH I don't recommend going to tour agencies to get their brochures for recommendations when it comes to Hokkaido. Hokkaido is huge and the attractions are spread rather far apart and the really nice ones are mostly quite inaccessible unless you have your own transport. Tour agencies have buses that bring you to those attractions but if you are going f&e, you'll find that it's rather difficult to take public transport to those places due to the infrequent bus timings. Meticulous planning will be required.
Best to head to Japan-guide instead. The time required to the attraction via public transport is usually stated there. They sometimes will also state the frequency of public transport as well. If you see something that says infrequent buses are available etc, then just drop it and look at some other attractions.