Now that we've added one written requirement for one class add-on (with a grandfathering option), we've perhaps added a complication.
You've a commercial f/w license and take the (old) ATP written say, today (6/29/14). You're grandfathered for the ME sim training requirement - through 6/30/2016.
Perhaps unwisely, you use the results to take (and pass) the ATP SE practical - let's say 8/15/2014.
Still grandfathered? You've taken the appropriate written within 24 months, but you've "used" it.
I'd guess the written "expires" when used for a successful practical, but I don't recall seeing any guidance. It hasn't really come up until this new ATP rule, at least that I can see. In the above case then you'd best bite the bullet and take the SE knowledge test and save your grandfathered results for the ME practical. It would be the safest course.