Side By Side View mode allows you to have two PDFs open next to each other. You can find the option in the View Module. 

Click on the folder icon next to each document selector in order to browse your computer and locate the files you want to open. 

Your files will open next to each other. By clicking on either file you will make it the active file, its name will be at the top. This will be the document that will scroll with your mouse wheel.  

You can turn on Synchronous Scrolling so that as you scroll with one file, the other scrolls with it. 

Click on Side By Side View again to turn off this option. Your files will remain open in PDF Architect as separate open PDFs.