A little late, but maybe this can help you:
You will make an automator workflow. Its quite easy:
1. First, open automator. (Open spotlight, e.g. by pressing command-spacebar, and type ”automator” without the quotation marks, then press Enter.)
2. From the promt, choose ”Workflow”, which should be highlighted.
3. In the search bar in the upper left, type ”Get Selected Finder Items”, and from the results below, drag the line with the same name to the grey area to the right.
4. In the search area again, type ”Combine”, and drag the entry named ”Combine PDF Pages” to the right, making sure it ends up below the earlier item.
5. Now, you are done. From under the File Menu (or by pressing command-S) save your workflow wherever you want to, and name it something nice (why not ”thx VickeVireG PDF merge”?) and then quit automator.
Now, whenever you want to merge PDF files, do the following:
6. Double click your automator workflow (”thx VickeVire G PDF merge”), which will open automator.
7. Now go to a folder containing the scanned pages (in PDF format) that you want to merge, sorted with the document containing the first pages first, and highlight both of them.
8. In automator, make sure that ”Shuffling pages” is chosen, and click ”Run” in the upper right corner.
9. In the lower left of the box named ”Combine PDF Pages” there is a button named ”Results”. Press it, and it will show your new file. Double click it, and it will open your PDF. Save it to wherever you want to have it.
I hope this works for you! Cheers!