Yes. In fact, we prefer this method to your uploading zipped files or folders.
Titles can have more than one file associated with them. For example, some publishers like to offer one PDF version in color for screen reading and a second PDF with fewer graphic elements and in black-and-white for home printing (i.e., a "printer-friendly" version). Of course, the latter effect can also be achieved using layers in Acrobat.
Some publishers will offer multiple formats for a title, providing PDF as well as Epub, Mobi, Power Point, or other formats as well. The customer can then choose which format files to download and use after purchase.
Maps and other add on components can be provided as .jpg files (commonly called "JPEGS"). For customer convenience, large maps can consist of a JPEG of the full map and/or individual JPEGs of the map split into page-size pieces for home printing. All of the map files can then be uploaded separately and then downloaded all at once by the buyer for easy delivery.
Unless a single title had more than eight or so files, we encourage you to upload multiple files for your title rather than zip all of the files together and offer one larger zip file. It is more convenient for the customer not to have to unzip their downloads, and it also makes updating individual files easier in the future.
Files for digital titles can be uploaded here.