Entering descriptive names for the two factors will make it easier to interpret your results.
If the two rows are labeled Male and Female, enter "Sex" or "Gender" as the name for the row factor. If two columns are labeled Control and Treated, enter "Treatment" as the name for the column factor.
If you have repeated measures, you can change the name of the repeated measurement block from "subject" to "litter" or "experiment" or whatever you want.