The polarity of a lumped port can be established in one of two ways. Differential ports have set polarity by definition. In cases where you use a patch, you can force the trace end of the patch to positive polarity by assigning the port attribute to both the patch and the end of the trace. When the port attribute is assigned in this way, RF3p orients the port polarity so that the trace is the positive terminal. If no polarity is indicated by the geometry, RF3p will assign the polarity based upon an analysis of the geometry. Nevertheless, if the polarity is important you should assign it yourself. The lumped port in the following image is defined with the port attribute on both the patch and the end of the trace, so this port has polarity with the positive end on the trace.
The following image shows the same system, where the port attribute has not been assigned to the end of the trace. In this case, the polarity will be defined by the solver.