it's mostly a matter of where you want to put your datum. for point masses, there is no limit to how deep in the gravity potential energy well you can go, however there is a limit to the binding energy between two bodies, namely at infinity where there is zero force. so people put the datum there and call it zero energy. if you potential is negative it means you're bound, if it's positive it means you're unbound.
what matters is differences in energy. in both models being at a higher altitude means you have more potential energy.
in addition, to make "balls roll downhill", the potential was chosen with a negative sign.
