I know this is an old post but I just setup Evernote on my Sony PRS-T3 Reader.
Do as follows on the Evernote website:
Activate 2FA
Goto your Profile
Security Summary
Manage Settings
Manage Application Passwords > New Application Password
Enter an alias for your Sony Reader
Click "Generate New Application Password"
Make a note of that password!
On your Sony Reader:
Evernote Setup
Enter your user ID
Enter the Application Password you generated earlier
You're in!