Due to the restriction of Chrome's downloads API, currently you cannot configure download folder inside the extension, you need to change Chrome's default download location and every downloaded file will go into that folder. Do as follows:
- Go to Chrome's Settings (chrome://settings)
- Click Show advanced settings...
- Change the Download location under Downloads section
With version greater than 0.9.0, you can find a folder button on status bar (bottom left) that directly opens above settings page.