Hi,
I think I might be getting confused but here's an example of what I'm trying to to do.
So there's the parent folder and within the parent folder there are two sub folders (pictured below). The subfolders contain several pdf documents. I want to run adobe to pull the all documents from the two subfolders at once instead of indiviually selecting each subfolder and then telling adobe to OCR them.

When I currently attempt to make mutliple files OCRs my current process tools -> select scans and ocr -> select mutiple files -> select only one folder -> hit ok and then repeat for as many subfolders as required. Is there way to automate this process by selecting all subfolders of the parent folder?
Yes, using an Action, as was mentioned before. You must have Acrobat Pro, though.
You'll find it under Tools - Action Wizard. Create a new Action, add to it a "Recognize Text using OCR" command and then a Save command, and change the Files to be Processed option to "Add Folder", save it and then click on it under the Action Wizard panel. You'll be prompted to select a folder. Select the parent folder and all the files in it, and in all of its sub-folders (recursively) will be processed in this way.