As I wrote, it doesn't really matter. As long as you apply the chosen directions consistently in the equations it will come out fine. Remember that there will be situations where it is not obvious which way the force will act, so it's rather important that it is not necessary to guess it correctly. (An exception to this is friction. You may sometimes need to consider two possibilities separately.)
In the diagram you posted, it's not always clear how a force is being defined. E.g. consider R2y. Is that a vertical force exerted by the girder on the base, or an (equal and opposite) force exerted by the base on the girder? Whichever it is, I assume R3y is defined similarly. Now compare R2y and R3y. You show both pointing down. They must be in fact be in opposite directions to counter the moment from the load.