APEX (Agricultural Policy/Environmental Extender model could be more appropriate for that purpose provided your 1 ha areas are not urbanized. In my experience, I found uncalibrated results from APEX more reliable than SWAT although both the models use similar methodology. APEX is more appropriate for smaller scale applications. For more information on APEX visit
http://apex.tamu.edu/
Runoff coefficients estimated using SWAT will be ok provided you calibrate and validate the model for the areas you are dealing with. For example, your 1 ha areas may be a part of a big watershed; If you calibrate the model for that watershed with available observations, you can use the HRU results to estimate runoff ratios for the areas you are interested in. Hope this helps
Exactly as Narayanan Kannan mentioned. If you calibrate the model for one big catchment and this 1 ha is a part of it then it will respond correctly. The problem with the small catchment is that all the parameters in model will be exaggerated and the output consequently would be unreliable.That is the nature of these types of models.