Each qube is a virtual machine, you don’t need a separate vm program. You generally use a conventional package manager (like apt or dnf) in a template if you want program to be accessible in many qubes, but other methods exist. Not sure what you mean by software section, check the docs to make it all clear:
Getting started - helps to wrap your head around qubes
Inheritance in Qubes OS - helps you decide where to install software
How to install software - official documentation, gives better explanation of how things work
Installing Software in Qubes (all methods) - more of a direct instruction