However, it is just recently that I configured my Brother MFC-7340 Multi-function to scan DIRECTLY to Evernote. Prior to this I was using my copier's scan to email function, which requires more steps.
Here are the instructions which can be easily adjusted to work with many other desktop scanners.
Start by opening the Brother Control Center from the taskbar or from the Programs menu. Click Configuration...
Choose an unassigned Custom Scan, give the button a name and pick SCAN TO IMAGE...
Now use the ADD button to create a new target application. Find the evernote.exe (evernote.app on a Mac) in your PC's Program Files. I choose .pdf as my preferred document type.
Once added, adjust the quality and interface settings as needed.
You are ready to scan to Evernote.