Boxes and virtual manager are frontends for libvirtd. With that being said, boxes is way more limited as it tried to work with little hassle. Boxes VMs run as the user so networking options are limited. For 3D acceleration you need to manually edit the config file. Just running windows with the virtio drivers in boxes works fine for me.
Long story short, if you want more advanced features like vfio and custom VM configurations use the command line or virtual manager.