If the PDFs are already on your iPad in other apps then it depends upon what those other apps support as to whether you can copy the PDFs from them to PDF Expert. The copy is initiated from the app that they are currently in, so try selecting one of the apps where you have those PDFs and see if that app has a 'copy' or 'open in' function which will copy them to PDF Expert.
Otherwise you can copy them via your computer's iTunes e.g. use file sharing to copy them out of their current app to your computer, and then from your computer to PDF Expert
File sharing : http://support.apple.com/kb/ht4094
Or you might be able to email them from your current apps and then use 'open in' on the attachment in Mail to open them in PDF Expert - but if there are a lot of PDFs as you imply then this may be slower.