>I read that freezing is recommended, but how do do you put so many frames in the freezer?
You put in however many will fit at a time.
>And how long do you leave them there?
24 hours is good.
>What's the best way to remove the small amounts of new nectar that was added?
Put them above an inner cover on a hive.
>Should the empty frames be bagged or otherwise sealed up during storage?
I wouldn't. I let the bees clean them dry, spray them with certan and stack them up in the apiary with a tight lid and bottom to keep the mice out.http://www.beeworks.com/uscatalog/details/certan.asp