Yes, the Onboard recorder is able to capture shots with 2 video channels. These are differentiated by a Channel ID, set in the Setup->Video menu of the recorder.
See this guide for details on recording ARRIRAW 3D: http://www.codexdigital.com/assets/downloads/CodexOnboard_RecordingARRIRAW3D_r05.05.11.pdf
The Media Stations software can then provide the master left and right eye files in separate directories with unique roll metadata. It can also transcode to 3D DNxHD mxf files for editing in Avid.
See this guide for details on the VFS: http://www.codexdigital.com/assets/downloads/Codex_software_UI%20-%20VFS_r30.09.11.pdf