By "proper orientation" do you mean this?
http://www.stovebolt.com/techtips/driveline/setup/index.html

Other than that you should be good to go, no need to remove axles but wouldn't hurt anything if you wanted to.

Grigg

•1951 GMC 250 in the Project Journals
•1948 Chevrolet 6400 - Detroit Diesel 4-53T - Roadranger 10 speed overdrive - 4 wheel disc brakes
•1952 Chevrolet 3800 pickup
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"First, get a clear notion of what you desire to accomplish, and then in all probability you will succeed in doing it..." -Henry Maudslay-