If he got sprayed in the face and is having problems I would seek vet care. While generally the spray is irritating to the eyes and nose by a burning sensation, usually only temporary, recently there have been more serious side effects found with skunks spraying dogs. In some cases it has been found to cause anemia which will show lethargy, weakness or discolored urine. For the eyes you may want to try flushing them with a sterile saline solution to take the sting out.
Here is more on this including making a mixture of household items to take the smell out. http://www.petplace.com/dogs/what-to-do-when-your-dog-has-been-skunked/page1.aspx