public class MetadataHelper{
    public String name {get;set;}
    public Boolean isEnabled {get;set;}

    public MetadataHelper(String name, Boolean isEnabled){
        this.name = name;
        this.isEnabled = isEnabled;
    }

    public String getFullName(){
        String fullName = 'Admin_Preference__mdt.';
        if(name.equalsIgnoreCase('Process Builder Preference')){
            fullName = fullName + 'Process_Builder_Preference';
        }else if(name.equalsIgnoreCase('Trigger Preference')){
            fullName = fullName + 'Trigger_Preference';
        }else if(name.equalsIgnoreCase('Validation Rule Preference')){
            fullName = fullName + 'Validation_Rule_Preference';
        }else if(name.equalsIgnoreCase('Workflow Preference')){
            fullName = fullName + 'Workflow_Preference';
        }
        return fullName;
    }
 }

So according to the above example – Metadata.Operations.retrieve() will retrieve the CustomMetadataRecord – Process Builder Preference. Now this record is having the label – “Process Builder Preference“, which we can get from the label field. The fullName of this record is – “Admin_Preference__mdt.Process_Builder_Preference” which we can get from the method getFullName(). 
In the above example, this CustomMetadata is having only one value which is stored inside a field of type Metadata.CustomMetadataValue. For that single  Metadata.CustomMetadataValue, the field = ‘Enabled__c” and value = true.

So the visual representation of the flow is –

With the above explanation, here comes to code –

Now to deploy the changes below is the code –

You can find the full code in my Github repository.

With all these changes, below is how the functionality working –