To specify more than one file in a given conversion task be sure to use a wildcard (*) in the Input Files entry box.
You can optionally save the output to the same folder as the input by simply checking the Save to Input Folder check box. This check box is only visible when you've already specified the input folder with a wildcard (i.e. *.DOC).
To do subfolders, be sure to check the Do Subfolders check box.
For example to convert all of the DOC files within the D:\MyDocFiles\ folder as well as the sub-folders you would enter the following for the Input File(s):
D:\MyDocFiles\*.DOC
Next select the Do Subfolders check box, and optionally the Save to Input folder check box. Click the Add button, then the Convert button. Depending on how many files/folders exist, the conversion task may take several minutes to an indefinite period of time.
More:
Quick Start - How to Convert Files
Quick Start - Special Processing on Files