Hi Subhadip,
Nice question, and it depends on what scale you are looking. If you look at (sub-)catchment scale, you would use the channel flow output of that (sub-)catchment. If you look at more detailed HRU scale, then you may want to use one or more of the surq_ outputs as well as lat and gw outputs. SWAT+ check provides the water balance info for the whole catchment for checking.
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