Deploy Software

I would like to have a feature like Run Tool but for Deploying Software. 
I would like to have the ability to upload setup files and correlated files like configs etc. 
I would like to have the ability to customise msi or exe command line execution parameters. It would be great to have something like PDQ Deploy and PDQ Connect feature in this tool integrated to allow instant deployment of customized applications.
I'm new user I currently under the impression that even if I upload complete set of file to Run Tool container and execute cmd or bat file that refers to other files in the folder it is not working for some reason.  It's like someone would implement that to just execute os sigle files and not whole set.