If you use Excel to make your CSV, it will insert CRLF line breaks (whether or not you are using windows, I believe). So you need to either just open in textedit and use find/replace to fix the line breaks, or use mac2unix or a program like that to convert the carriage returns.
So Excel is okay — just make sure to convert the line endings.
This will be an issue with making sample metadata files, too, not only manifest files.