I'm not exactly sure what you are asking. If you want NHD flowlines to match those used in SWAT, then you can of course "burn in" that flow-line data set before the watershed delineation step. And if you want subbasins to terminate at the outlet of a lake, then you can add an outlet at that point in ArcSWAT (and if you want subbasins of inlet streams to terminate where they enter the lake boundary, add outlets at those points also).
Lakes are usually modeled as reservoirs in SWAT, not as individual HRUs. Small areas of WATR land cover are aggregated into a water HRU but these do not contribute to the loads from the subbasin, if I recall. If there is enough area of WATR in the subbasin to affect loads, then they should be modeled as a pond or wetland feature in that subbasin.
-- Jim