The boxes cost about $1.40 each for a pack of 20 and about half that for a pack of 200. I think they are supposed to be used to get the flat rate. 

Items purchased seperately are supposed to be sent seperately and if cases are opened against you for each seperate order you will only be able to provide proof to ebay for one transaction. The same tracking number can usually be uploaded to different orders, but may not be possible in an open case.

The lables print out easy enough, I find it a pain to do when there are only one or two. I use the 500g and 3Kg satchels as well, there is also a 1KG express satchel availbale now. I buy all my satchels on ebay (form 3rd parties)  which usually saves about 20%, coupled with all the vouchers ebay hands out it becomes quite a bit cheaper.