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I would like to merge 9 single page pdfs. This will be a something where there will be thousands of pdfs, but we need in multiple of 9 pages, then I am going to apply a template. Am I using the correct configurator? Merge PDF... please help.

You are, but since there will be thousands of PDF's you first have to assemble them into folder based on some logic, before running Merge PDF.

I am using Assemble job, Arbitrary Files placing them in a folder with 9 single page pdfs. How do I tell the Merge PDF to merge the file within each folder that Assemble job makes?
TIA

Sorry, I am not sure I understand.
You don't have to tell anything to Merge PDF, it merges all PDF's into Single PDF from same folder by default.
There are no other options other than if you want to keep page labels or not.
With Assemble Job you control what and how you want to merge.

I figured it out. I needed Assemble Job then Merge PDF - and it worked beautifully.