If it has a hole in it then have a hole if it doesn't then don't worry.
There are plenty of types of canopy, some have holes others don't. As John mentioned the hole was there to prevent the instability of canopies (basically chopping from side to side uncontrollably made it difficult to land without breaking things), they added a hole in the top which prevented this, however it did not prevent line over, the skirt was added at a later date to help prevent line over. If you have mesh panels in the canopy as opposed to or inclusive of a skirt they are really designed as drive panels giving the canopy forward momentum and they can also be steered.
If the canopy has no hole raise it a little higher. If your fire is smokey use drier wood. If you step back from a canopy with no hole when you have a smokey fire you'll notice a couple of things. One is the amount of smoke escaping from the skirt and the other will be the amount of smoke that actually permeates through the material in little wisps. Canopies without holes normally allow greater airflow through the fabric and tend not to be waterproof. They will still keep the majority of the weather off though.
If the canopy you have is a PX4 it will have 32 separate panels and 32 corresponding rigging cords. Mark cords one, nine, seventeen and 25. This will give you the four corners of the chute (if you wish, north, east, south and west), setting these out first when setting the canopy up makes life easier.
Don't cut off the cords, you may not use them all every time you set up, but if one gets damaged you'll be happy to have spare. Hank them up and tie them off.