So, in short, the Macro Editor form control is the one that is used for transformations in Kentico 9.
If you want to create your own way to input info like transformation data, then I would recommend checking out the DocumentType_Edit_Transformation_New.aspx file which is how we currently do it. This file uses the TransformationCode control to input the data. Next checkout the TransformationCode.ascx file. The line that holds the transformation info is
<cms:MacroEditor runat="server" ID="txtCode" ShortID="e" Visible="false" Width="100%" />
Which is the form control where you put the content. If you want to know how the transformation is stored, you can see this by going to the Modules application and opening Modules -> Design -> Classes -> Transformation -> Fields. The TransformationCode is the field storing the actual content.