If you had two PDF's, they would both have unique titles, yes? If so, then they would be listed uniquely in the reference, but remember, you can group references when citing, ie. [1, 3, 5] or if 1 to 5 was applicable for a statement [1-5].
The only way I know that you could physically join two PDF's is if you have the original text document, or, you print them both out and scan them in together as one document, PDF scanning via most scanner softwares these days.
I would think they would both be written by different people, hence the author issue, so would require to be listed uniquely! Yes / No?
Ok, if you look at the example page, you will see two galleries. The first one is uploaded just using the image sizes at different heights, widths, etc... the software will do the work, yes, but you can see that they are different heights, as the width is automatically controlled. If you want them to look pretty when the software controls the resizing, aka, the second gallery on example page, then you are first best to resize / crop every image so they are the same size, then you get a much nicer looking gallery when you upload.
If you don't have the ability or software to crop / resize images, then just upload them to the folder name as stated, then send me a PC with the folder name and I will download them onto my PC, crop / resize them all to the same size, reupload over the existing and it will automatically fix itself.
Pretty much, the smallest image will define the rest, however; if scaling is used correctly, you can have different image sizes providing they are proportionate in scaling. Best of just to make all to the smallest size.