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If you set domain enviroment you can use domainenv.cmd and WLS environment for setWLS.cmd
It depends what you want to do with WebLogic - they can serve different purposes.
If you want to run WLST scripts against a domain, use setDomainEnv.sh/cmd
If you want to run scripts against the ORACLE_HOME of WebLogic, use setWLSEnv.sh/cmd.