One possible approach to calibration is to convert your data to a monthly format. However, this method may result in the loss of important information from your measured data. An alternative approach is to run SWAT on a daily basis, extract daily data using the No_Observation option in SWAT-CUP, and then convert the daily output to a bi-weekly format. You can then compare the bi-weekly data with your measured data. To accomplish this, you will need a program that converts the daily SWAT output to a bi-weekly format.
In my first SWAT application (the Thur Watershed in Switzerland), I also worked with bi-weekly data and applied the method described above.
It would also be valuable to calibrate using both methods (monthly and bi-weekly) and compare the results. This comparative analysis would make the study more robust and could enhance the quality of the paper.