You can certainly top-and-tail bikes on the roof so they are each facing alternating directions, this will help you fit as many bikes as possible on your roof bars without the handlebars clashing (up to four bikes on most 'though' style roof bars). Most bike carriers will allow you to slide the fittings off and turn them around so they are still facing the side you need, so it's easier to fit and load the bike. Check the instructions to see if this is possible for a particular bike carrier.
You'll also need to make sure you don't exceed the maximum weight for the bars and your car roof loading limit.