It's being done both ways. Some believe the passenger side goes to the top and others the driver's side to the top. I put the driver side to the top as at that time, that is the way Lonny suggested.
The flow comes from the passenger side and returns on the driver side. There are debates as to which way is the best way but I don't think in the end it really matters. Lonny said some of the first cars had issues with air getting trapped at the top when the passenger was connected to it. So the idea was to push the fluid up along with the air and out the top. The suggested may have changed since our build. We have absolutely no issues with temps!
Others believe that most manufactures flow down as the water cools so it should enter at the top. You decide which way you want to do it