From the PA Turnpike's website
http://www.paturnpike.com/news/2004/workstopnoncom.aspx
After midnight:
All E-ZPass customers will pay a MAXIMUM toll of $2 for passenger vehicles and $15 for commercial vehicles. That is, if the standard toll is LESS THAN the temporary flat toll, E-ZPass customers will pay the standard toll.
So no need to put the EZPass away, just leave it on and you can still pay the flat fee.