If you have already added and configured the equipment in the equipment manager, when you log your training you just select the shoe that you ran in and save and the km's will start to be totalled.
Though let me know if you were asking something different.
To dovetail on the above question.... If I add a peice of equipment (shoes) that I have been running in since January, is there way to have the site back count all the running miles or do I have to manually go back to each run workout and add the shoes?
You have to manually go back and update those workouts tagging the shoe...OR...use your log reports to figure out how many miles you have on the new shoes before you added them to the tracker and just 'add' those miles when you configure the shoe.