The messages folder will automatically keep a copy of everything unless you change to SMS and Email Inboxes - Separately. (Other options are combined or theme controlled.) Note that if you have multiple email accounts, all emails will show in the messages folder. I keep the messages folder and rely on the separate email folders for each account but somepeople like the combined folder. (This is how my personal BB on BIS works.)
I believe if you are on BES, you only have the Messages folder for your BES email. My work phone doesn't allow personal email accounts to be added but I think if you are able to add your personal emails, they also go to the Messages folder as well in this case and that there is no way to keep them out or to set up a separate folder containing only the BES email. I think you still have the option to separate the email and sms messages though.
The most recent OS (firmware) for the 8900 should be the one listed in the sticky at the top of this forum. There may be beta versions available elsewhere, but on BB forums, the versions listed are the latest one released by a carrier and you should be able to use it on you BB, regardless of who your carrier is, by following the instructions in the first post of the sticky.
Edit: Sorry, thought I was in the 8900 forum instead of the General. Should have said the latest OS will be in the sticky at the top of the model specific forum, in this case, the 8900 forum. http://www.blackberryforums.com/gene...ssion-javelin/