If I recall:
-- make sure all your missing values are filled in with a -99.
-- assuming you have a nearby weather station with all the required statistics in the database, SWAT will fill in missing values by using its weather generator. This is automatically (generally) available for watersheds in the USA.
-- however, it is not good practice to have missing precipitation (P) values, assuming you wish to calibrate your model to known flows. You are usually much better off finding some way to fill in the missing values with data from other nearby stations. While the weather generator may produce statistically reasonable P values over the course of a year or so, there is little chance it would fill in something close to the actual amount for specific days with missing data.
-- I generally make sure my data are complete for P, minT, and maxT, and simulate everything else (again, for watersheds in the USA)
-- Jim