For some reason my monitor will only work with the card in the second card slot on my board. I think it might have to do with the slot being the first full 16x slot on the board though. I would just boot the computer with it plugged into one, and then switch it out with the pc still running to see which one gets detected.
You can adjust the default values for GPU priority in your BIOS settings. Just need to tell the computer to use your MOBO's on-board GPU, rather than the MSI's.
Don't forget your dummy plugs for when you start mining
![Smiley](https://bitcointalk.org/Smileys/default/smiley.gif)