Endpoint Protection

Does SEP scan every file that gets uploaded to websites such as DropBox or Box.com? If so, this would really bog down the actual files transfer and upload speed and how would I address this?

By default, Auto-Protect scans files as they are written from your computer to a remote computer. Auto-Protect also scans files when they are written from a remote computer to your computer.

When you read files on a remote computer, however, Auto-Protect might not scan the files. By default, Auto-Protect tries to trust remote versions of Auto-Protect. If the trust option is enabled on both computers, the local Auto-Protect checks the remote computer's Auto-Protect settings. If the remote Auto-Protect settings provide at least as high a level of security as the local settings, the local
Auto-Protect trusts the remote Auto-Protect. When the local Auto-Protect trusts the remote Auto-Protect, the local Auto-Protect does not scan the files that it reads from the remote computer. The local computer trusts that the remote Auto-Protect already scanned the files.
 

The solution is disable auto protect ( not recomnded) or create exception for auto potect.
 

When you access any files from your machine or netwrok share autoprotect scans it by default. these settings can be modified using the AV policy. This setting shouldn't cause any issues while uploading the files on legitimate websites.