Welcome to BBF.
Please read your user guide and read through our FAQ for additional information.
1. Email comes to the general messages folder and to the folder for the specific email account. If you delete a message from one folder, it is deleted from both. That cannot be changed. You can hide the one that you do not want to use, but I do not suggest hiding the main messages folder as that also receives missed call and SMS notifications. If your device has OS 5, which I think the 9700 does ther ei a method to separate it out. This might be the way to do it:Messages > Options > General Options > SMS & Email Inboxes = Separate. Use the SEARCH feature if not.
2. Email does not sync. Only mail received from the time you set up the account on the BB will be pushed to the device. If you need old messages, then you will need to send them to yourself.