I found that replacing the original SAP logo is the best solution.. since uploading our custom logo in the theme designer is not working..
this can be done by:
Go to (SE80 -> MIME Repository) under the path /sap/public/bc/ui5/LIBRARIES/VER/lib_version/com.sap.ui5.core/META-INF/resources/sap/ui/core/mimes/logo/
then replace the logo image with your custom one.