Having venting or holes in your rig is typically not a big deal 99% of the time.
To install them simply put them in place and use a screw on the top part to hold it there. Notice that you will need a PCI cover, and not a bend-to-remove slug for this to work. If you really want it covered then just about any kind of tape (preferably metal/foil ducting tape) will do the trick.
As a general rule of thumb, if your computer is in a location that is fairly dust free then it does not matter if your case is perfectly airtight. Personally I run a high-end system with very low air flow (due to noise concerns), and so I have concerns about having airflow directed at specific places and taking a certin route within my computer, so I have all extraneous holes blocked off. But honestly it is more to fulfill my own neurotic tendencies rather than really netting me any extra performance, and as all of my fans are low RPM there is not much in the way of a dust problem.
I guess all of that to say: If you have them, great. It will make your system look nicer and less thrown-together. But it probably isn't doing much of any harm being open either.