Checks and balances work both ways

"The executive branch shall construe these sections in a manner consistent with the constitutional authority of the President."

The President's Statement on Signing of H.R. 2863, the "Department of Defense, Emergency Supplemental Appropriations to Address Hurricanes in the Gulf of Mexico, and Pandemic Influenza Act, 2006", makes it clear that this President understands his Constitutional authority, and will not be bullied by Congress.