Hello Nick,
We have a free tool for our customers that enable them to concatenate / Append pdf files together. This tool is called PDFConcat.exe and is available at:
http://www.amyuni.com/en/support/downloads.html
This tool will work with all pdf files generated by our driver, but it may not work with some pdf files generated by other products.
Concerning your second question, yes, there is a way to automate the creation of pdf files. In fact, if you have an application that generates reports lets say, you can let your appliation generates these same reports in PDF format and same them to disk without any user interaction using the Developer version of the PDF Converter.
For more details about using the driver from inside your application without user interaction please download any of our technical notes from:
http://www.amyuni.com/en/support/technotes.html