We've released an update to Synaptive Streamnotes which includes the ability to add custom notes to items you save to Evernote, OneNote or when your save PDF/CSV files.

Select the destination you want to save to, and then simply enter text in the Notes text box. Next, click Save to... and the text will get added to the item you're saving:

More information on Streamnotes is available on the Synaptive web site.