After tinkering around for over an hour, I coded a way to properly sort all file types, as the default rules in Chrono Download Manager do not work.

Examples for rules:

Condition
[ext_video].has(*ext*)
*ext*.is([ext_pdf])

Naming Mask
video/*name*.*ext*
pdf/*name*.ext

Notice I ditched the {r_done}&& because that was literally breaking the filtering. Also, although it doesn't matter as much as I thought, it was more logical to test if a long list of extensions in a string ".has" a certain extention inside of it. Thus you'll see ".has" used except for ext_pdf, because it's a single extension only, which I removed from ext_doc and made separate. 

I'll attach screenshots of my setup so you can get this tool working properly. I haven't bothered to learn more about it for now since it's working.