CiscoWorks supports non-Cisco devices in only the most rudimentary ways - very basic config management and sylogging is all I can think of. Versions prior to 4.0 will also count those non-Cisco devices against your license.It is really designed to exploit the capabilities and integrate with Cisco devices and the software they run.
If you have signifgicant non-Cisco installed base you may want to consider other products. If all you need is configurations, RANCID is fine in a multi-vendor environment. Solarwinds Orion and What's Up Gold (licensed commercial products) are often used for monitoring, as is MRTG and/or Cacti (open source).
