Upgrade CCP 3.0.6 to 4.2
The upgrade should be in the following order
>>>if the second, so can I run CPBM (2.1) on CCP 3.0.6 and Xenserver 6.1 for a while before completing the upgrade?
Yes. You can check the supported CCP versions with CPBM 2.1 here http://support.citrix.com/proddocs/topic/cpbm-21-map/ccpb-ccp-conn-wrapper-con.html