BookBaby requires a high resolution PDF file with all fonts embedded and all links activated (internal - TOC, external - web links, etc.) in order to convert into a Fixed Layout eBook file.
We can also accept a packaged InDesign file (a zipped file of the document that includes all fonts and images).
It is also possible for you to supply us with an epub file HOWEVER, if you want your fixed layout book to be able to be distributed via Amazon, you would still need to supply a pdf or indd.