Bikelague.org published this (below) on the bill- they will probably be the ones to listen to on this because they are in DC and they lobby Congress on behalf of bicycling. They are working to figure out how the provision will be implemented.
Bicycle Commuter Tax Provision Passes House and Senate (10.03.08)
After seven long years, the bicycle commuter tax provision has finally passed both the House and Senate as part of the financial bailout package. President Bush said that he would quickly sign the $700 billion bailout bill. Thanks to all of you around the country who have contacted your congressional leaders over the years, and also thanks to Congressman Blumenauer and Senator Wyden for their continued insistence on having this benefit provided to bicycling Americans. Keep checking back here as we work on the implementation process.