Cut them to length, cover with bunk carpet (make sure carpet doesn't completely cover the bottom of the bunk...this allows water to drain from carpet better) and staple with stainless steel staples, drop boat in water, change out bunks at the launch, and load the boat back up and head home.
I've never had this issue, but at least one knowledgeable lister here will tell you to avoid using treated lumber. Something about the new chemicals approved by EPA for preservation of wood in residential uses being highly incompatible with aluminum hulls. Pick up some 9' 2x4's, install some marine carpet (Home Depot/Lowe's sells that stuff too) using monel rust-proof staples and carpet glue and you should be good to go.
FYI, disclaimer - I did use treated wood, but with carpet AND a painted tin hull, I figured I was willing to take the risk.
Check the "More" menu above, then go to Grab Bag, John from CA did a GREAT detailed document on this, including pictures and supplies! i've done it for my Tracker and Nitro, its PERFECT!