Well... after searching the forum some more, I found that indeed CWW v6.1 will not backup the configs but the follow-on product will: Small Network Management Solution, SNMS.
The upgrade package for CWW6.1 to SNMS v1.5 is CWSNM-1.5-WINUP-K9 CiscoWorks Small NMS Solution upgrade for CWW 5.0, 6.0, and 6.1 customer.
http://www.cisco.com/en/US/products/sw/cscowork/ps2408/prod_bulletin09186a00801c0a33.html
But you can also try Kiwi Cat Tools. Look at:
http://www.kiwisyslog.com/cattools2.htm.