Most shocks either have an allen key, 5mm I believe on Bilstiens, or a squared off top on the shock so you can get a Cresent wrench on there, I think that is what the stock shocks had. You hold the allen key or wrench while loosening the nut.
Replacing the shocks won't have any effect on the alignment. The rear shocks come right off and on sitting on the driveway. It is a lot easier to do the fronts by putting the front of the truck on a jackstand and removing the front tire.