You'll find many affordable recommendations at
http://twenj.com/swisshtl.htm In the mountains you'll be visiting
during the off-season so many of the regular hotels will be closed,
but most or all of the budget-conscious choices are open year-round.
You'll find an overview of information for visitors to Switzerland beginning at http://twenj.com/swissvisit.htm including our ideas about some of the more important (more enjoyable) places to visit as well as links to many other sources of information.
Public transport is unbelievably (to most North Americans) good in Switzerland. For most itineraries this is the way to go. The Swiss Pass is an excellent deal. You'll find extensive info on traveling by rail (and boat, cable, etc.) at http://twenj.com/swissrail.htm