Someone else asked this question during the webinar tonight - if you want to submit multiple transcripts, you'll have to upload them as one PDF file (so probably print each transcript and scan as one document). The staff gave conflicting answers for including coursework from other institutions where you did not earn a degree, so I'm not sure what they want.
pdf mergers! Just google it. There are so many free ones.
PDFMerge! - Merge PDF files online for free