this is what i do when i bottle.
make sure all the bottles have been scrubbed free of any residue or nasties on the inside. i usually do this as i consume the beer in the bottle, simply rinse it out and put it aside. sometiems if i let the bottles sit for a spell, i soak them in bleach water adn scrub them out with a bottle brush, then rinse them.
on bottling day, i put them in a big bucket full of iodophor... take them out of the bucket as i need them, pour the iodophor out, and shake it a few times to get any left overs out, then bottle.