Right way to analyze lage area DEM

[xwq0371]

Thank you for the great tool in advance.Recently, I ran into this issue and I would like to get some suggestions.

Right now I am doing a analysis on a large area of dem, like 4km x 4km, I find out that there could be multiple watershed thus multiple outlet points is generated. I am wondering if applying analysis to each watershed with different outlet point,then patch them into one is the right way to go or not.Since I tried to just use one of the outlet points to do the analysis regarlessly and the result is not that differentiate from the separate analysis I mentioned above, for my study case, the losses is accpetable.