It's simple once you get past fiddling with pixels.
Guidelines for U.S. Passport photos are here, http://travel.state.gov/passport/pptphotoreq/pptphotoreq_5333.html
A photo template is here unless they've moved it, http://travel.state.gov/passport/pptphotoreq/photocomptemplate/photocomptemplate_5297.html
The easiest way I found to align the picture perfectly, is to make the photo portion of that template into a 600x600 pixel square in Photoshop. Here is that Photoshop file with the guide already there.
Paste the subject's photo as a new layer on top of the template and take the opacity down to 50%. Use Free Transform to make your photo the perfect size and alignment to match. Then raise the opacity back to 100%.
Here's a random portrait snagged from MS Clipart, which isn't a good passport photo (not plain white background, not looking at camera-- see, I'm getting good at this!) but it'll work for an example.
Select the whole square and copy, then paste it into another Photoshop document set up at 4" x 6". Here's that Photoshop file at the right resolution with guides to help align the photos.
Three of them fit nicely on a 4x6" photo which can then be exported and be printed for seven cents at Walmart. Two for the passport office and one in case you make a mistake in cutting :-)