Unfortunately it is not possible to use agent and agent-free approaches at the same time on different target machines. For example, to use only agent (service) scan, you would go to "Options - Scanner" and enable the option "Disable the RPC protocol for scanning of Windows computers". To use only agent-free (WMI) scan, you would need to rename or remove the file "tniwinagent.exe" in the program's installation directory. But it's not possible to use both these approaches simultaneously, or specify which one should be used on which computers. Perhaps we can add such possibility in the future.
Take note that the agent-free WMI scan collects more information than the SNMP scan (besides the fact that SNMP-collected information is not structured), and the agent (service) scan collects more information than the agent-free WMI scan (like disk drives S.M.A.R.T. data, memory modules SPD data, etc). So the agent scan is recommended, and should not cause any problems.