Couple of questions: Do these scratches go deeper than the clear coat (many cars these days have a clear coat applied over the colour coat)? Have they penetrated past the colour layer to the primer? Do they go right to the bare metal?
Depending on which or how far they go, there are various things you can do:
1) If it is just the clear coat, you can probably just buff it out with rubbing compound.
2) If the colour layer is marked but not penetrated you could probably spray some clear lacquer over the scratch after a light sanding with 400 grit wet sandpaper. If you're doing this you are trying to feather out the edges of the scratch so that you have a smooth indent as opposed to a gouge.
3) If you see bare metal you will have to feather the whole mess out. Remember you don't want to paint over the clear coat or put primer over the colour. If you just have a colour coat then you will have to sand that away until you see only primer, apply the primer over the bare metal, then when that's dry, apply the colour over that.
If you're going to use one of those colour markers (from canadian tire) only use it if the scratch doesn't go down to the bare metal. They don't adhere well to bare steel. If the scratch doesn't go to bare metal fill the scratch with the marker (so the colour is higher or thicker than the original paint) then you can feather it down with 400 or 1000 grit sandpaper and polish the whole area with rubbing compound.