The second building to the left as you enter the base contains an officer and a lowly mechanic of some sort. You can chlorophorm the officer and then knife the mechanic. Switch uniforms with the knocked out officer.
There is a large bin or open top box of some kind next to a large drill or press machine or whatever it is. You can carry a body over to it and then throw them off of your back with the right mouse button.
Saves a trip to the truck and nobody is the wiser outside. Just be sure to check on the location of the primary target. He has a habbit of showing up just as your undressing. Awkward to say the least.
On the higher difficulties it seems to be much trickier to get close enough to use the chlorophorm so make sure you have plenty of time and save before making the attempt.
Once your dressed and have thrown the bodies in the bin, the rest of the mission is fairly straight forward.
I recommend disabling the alarm right after obtaining the uniform. Its on the top floor of the office bunker. It can help if anything goes wrong later on during the mission.
Good luck