Do you want to prepare observation series of data in to SWAT-CUP format?
The model is said to be calibrated after adjusting the observed data in to appropriate SWAT-CUP format,
Running either of the 5 SWAT-CUP packages, and
Fixing the optimum model parameters which results relatively higher model performance rating criteria of interest, NSE, R2, KGE, MNSE, bR2...
Then you will choose the final SWAT-CUP run and that result is the calibrated model simulation result.
Attached find a .xlsx file with formats to convert observed data in to SWAT-CUP acceptable format. You can past your data in to the spreadsheet and run SWAT-CUP.
I have also attached a SWAT-CUP file for you to easily look at where you should make changes.
I have attached the SWAT-CUP SUFI2 formulation. For the rest of the calibration uncertainty analysis techniques, you may refer the following paper. As you may choose any of the available SWAT-CUP packages (DOI:10.3390/w9100782).