As you have three devices, each one separately generates the sound. The only thing common would be the sound itself, such as a wav or mp3 file.
When you use the PC's sound chip (VIA HD) that is one hardware device and the wired on the motherboard output jacks. If you use a USB connected sound device then you are using that device to generate the sound and that device's physical jacks. If you use the ATI HDMI, most video cards have their own built in audio chip (unless this is an old video card that uses S/PDIF connection to the motherboard) and thus again everything separate for audio generation and connection.
One comment, if you have both the Via on board audio and the usb connected sound card enabled at the same time there can be conflicts and sound problems. Not the balance problem you have but there can be problems. If you want to use the VIA then physically disconnect the USB. If you want to use the USB, disable the on-board audio in the BIOS.