As for how to upgrade them... You'll need to write scripts that take into account the architecture of each os, among other variables.
http://docs.splunk.com/Documentation/Splunk/6.2.0/Forwarding/UpgradetheWindowsforwarder
http://docs.splunk.com/Documentation/Splunk/6.2.0/Forwarding/UpgradetheNixforwarder
http://docs.splunk.com/Documentation/Splunk/6.1/installation/HowtoupgradeSplunk
For windows, i've used winrm and powershell remoting. For linux I've used everything from bash scripts to python.
As for compatabillity between versions:
http://docs.splunk.com/Documentation/Splunk/6.2.0/Forwarding/Compatibilitybetweenforwardersandindexers
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