Last time I re-arranged the tank I left my bettas in their tanks, but I worked around them. Which was rather interesting 'cause they're too curious about what I'm doing LOL.
I move my plants around alot. Everyweek to be exact when i change the water. I think it makes the fish less agressive. Mainly the to male mollies hehe. It also keeps my gouramis from getting to touchy.
I move the decor about most water changes too. I have a red tailed shark and a ruby shark that I think get along simply because they dont have time to set up a territory!!