The File Upload fields inside the questionnaire are designed to hold as many uploads as the recruit may need to submit on the questionnaire within one field. Each File Upload field will have a "+ Add File" that will illuminate below the uploaded documents after upload is complete.
The recruit can click this to get a new row to upload into, so you do not need to add multiple File Upload fields into the questionnaire in order to capture multiple documents of the same type (e.g. Transcripts from all schools).
You can add multiple types of file upload fields if you would to your questionnaire organized in that manner, or have one file upload field for all documents. As an example, you could create one file upload field for Transcripts and one for Test Scores, or you could create one File Upload field labeled "Upload All Academic Documents" and put in the instructions "Upload all Transcripts, Test Scores, and other Academically Related Documents here."