You need to install the Contact Form 7 plugin in order use a custom template for embeddable forms.

For a quick demo see: http://demo.wpfilebase.com/embedded-upload-form/embedded-upload-form-with-custom-fields/

1. Create a contact form defining the custom fields you want to use. The names of the form-tags have to  be equal to the template variables of WP-Filebase files, otherwise the entered data will be lost. You find the list of template variables here. For example if you want the user to enter a valid email and save this as file author use this tag: [[email* file_author]]. Do NOT use the automatically generated names like [[email* email-641]], data the user enters here will be lost.
2. Create or edit a embeddable form in WP-Filebase dashboard. Chose the created Contact Form 7 Form and untick “Use advanced Drag & Drop Uploader” (by default unchecked).
3. Insert the form in any page using the WP-Filebase Editor Plugin that appears in the visual editor when editing a post or page