My husband and I went to Germany in August 2004. We didn't bike there - except for a tour of Munich on cruisers.However, cycling is very popular and the bike paths were easy to spot. The entire transportation system, including bike paths, is well set-up and well maintained. The maps we picked up over there for our travels were easy to use and up to date.
Sounds like you're in for a great trip. We went to Bavaria and spent time in the Alps which were beautiful. I'd love to go back sometime.
Enjoy!
Deb