Yes, with rare exceptions. In fact, uploading directly from version 6 of the Pesticide Reporting Software (Options , , , or D (installed version) ) is the quickest and easiest way to submit your report.
Click the Upload Report To NYSDEC button on the Control Center and follow a few simple steps. See How to Submit Files to DEC on the Help menu for more details.
The exceptions? Some users in a tightly controlled enterprise environment might not be able to use the direct upload method. If that is the case, then you may upload your report through the website.