Happy to answer. I always use the auto focus. Canon has such a superior autofocus system than Nikon that its a no brainer. Easiest way to tell the difference is to stand at the end of the runway at say Nellis or Leemore and shoot a fighter coming towards you. The Canon system will have no problem refocusing on the image as it comes towards you, the Nikon on the other hand finds it impossible. One of my editors is changing from Nikon to Canon because of the superiority of the autofocus system.
I have also found that the Canon bodies tend to stand up to hard knocks much better. Good example was when I flew with one of the Kelly brothers in a Tomcat from Pax River. Did a cat shot from the runway there, had my camera down beside the left hand side of the seat but not all the way back. When we went thru the cat shot it threw the camera back and a nice chunk of it went flying across in front of me, stupid me for putting it there in the first place, but I just picked it up and it kept going. Have taken them out in the desert, up in the mountains etc and they just keep going.
It all comes down to personal preference and I have found the Canon 1 series suits me best. Feel free to ask any questions, always happy to answer.
Regards
Ned