how does your billing company want to receive the invoices? will they accept a delimited text file as a submission or do they need a electronic printout (saved PDF)? this makes a difference in your approach to the problem.
Either way, secure FTP is necessary for either type of transfer. Printing to a PDF file is possible with programs like CutePDF or Adobe Acrobat Writer. This is how you get the "printout" into electronic format so you can send them encrypted via secure FTP. There are many products for secure FTP, WINSCP is just one of many. If they will accept a delimited file, this will save you a few steps.
