If you're interested in the Alpine trail route, then check out the Google Earth file that Bubbles posted on the "
Swiss sightseeing via satellite" thread.
I've also been gradually working my way across the country by linking together separate one-day hikes. I looked at the Alpine trail route, but decided that in many of the sections, the official trail takes a relatively easy option, hitting many of the passes and not too many of the high-points of each region. I've therefore been picking out my own routes, which is quite easy to do with the extensive Swiss trail system.
So, my advice would be to put together a route by yourself that hits the kind of terrain that you're looking for, and possibly using an established long-distance route like the Alpine trail as good advice/suggestion/starting point.
I generally only use
the 1:100,000 composite maps from Swiss Topo, they are good enough because the trail signage is so excellent. Occasionally I get a little confused, and sometimes use trails that aren't marked on that map, but that is all part of the fun. Using those maps is WAY cheaper than buying the 1:50,000 maps for each region that you want to hike in.
In addition to the maps, I often check out the area by flying around it in
Google Earth to decide exactly which trail to take. One more web resource is
SwissGeo, which has the SwissTopo maps online (just type in a place-name or post-code) but you can only see a small section of map at a time. However, you can use the site to zoom in and get details that you cannot see on the 1:100,000 or 1:50,000 maps, so that can also aid route planning before leaving home.