Hello. When we upgraded our power supplies on 6506, we didn't have any problems. Just wait until the new PS becomes operational (all LEDs ok, syslog says that everything is ok, and check "show environment power" command output), and then replace the second one.
But don't delay, as system does something depending on your set up.
Here are the actions:
http://www.cisco.com/en/US/customer/products/hw/switches/ps700/products_tech_note09186a008015bfa8.shtml#power_red
And here is the procedure:
http://www.cisco.com/en/US/customer/products/hw/switches/ps708/products_installation_guide_chapter09186a008020e0f8.html#wp1093622
Standard turn off, unscrew, replace, connect, power on...
Hope this helps.
Please rate all helpful posts.