I have a VGA and HDMI output on the video card and DVI and VGA on the motherboard. I read that DVI is better than VGA but if it's not coming out of the video card what will be the effect of using it instead of the VGA from card?
The only things that come to my mind to worry about are devices* that require an HDCP handshake, in which case you'll be required to use HDMI/DVI connection. There are also some limitations on the resolution and refresh rate coming out of your VGA Port, but most of this is card dependent (and you're probably not going to be affected).
If your issue is simply that you don't have a monitor that can accept HDMI consider using an HDMI to DVI Cable, they are relatively cheap, the only practical downside for your usage being you lose the Audio Channel on your HDMI port.
*Edit: By devices I meant to say Software.
1+1, And the specific case where the HDCP handshake matters is if you have a Blu-Ray drive in your computer and want to play a disc. Without HDCP the playback software will not play the disc, VGA will NOT work for Blu-Rays. DVI and HDMI support HDCP while VGA doesn't.– headkaseDec 7, 2013 at 5:05
As far as the underlying video signals are concerned, DVI and HDMI are effectively the same thing (HDMI optionally adds audio signals, and has a crappier connector). Adapters to convert one to the other are cheap and plentiful.
HDMI and DVI are both digital video connection standards, as opposed to VGA which is an analog connection and starts to get fuzzy at higher resolutions, especially when using cheap cables. So, where possible, the digital connection is preferred.