Essentially, you can use the special rate or choose to calculate each local meal allowance based on each over night.

You can deduct anything that is above and beyond what your employer provides.

IE if you get $35/day per diem, but the standard meal allowance for the city you were overnighting in was $47, you can deduct the $12 difference. (or if applying the standard special rate for transportation workers, you can deduct $59 minus the $35 your employer paid you)

Depending on where you travel, the standard rate might be better or taking the time to figure out each local allowance might be better. (For example the standard allowance for meals in New York in 2013 is $71/day, so if you did a lot of NYC overnights, it might be better to calculate all of your overnights instead of using the standard special rate.)

Whichever method you choose though, you have to use for the entire year, so if you use the special rate, it applies to all of your overnights. If you choose to determine each individual locality you have to do it for all of your overnights.