-- you can place the reservoirs manually in the proper subbasin during the watershed delineation process when building the model
-- you do not have to input the reservoir boundary. All SWAT really cares about is the area and volume. SWAT presumes the reservoir is at the outlet of the subbasin. Hopefully, your subbasin has an area of land use (and "soil") corresponding approximately to the area of the reservoir. These areas of WATR land use do not contribute runoff or loads from the subbasin. They are then replaced with an equivalent area of reservoir, where water balance is tracked explicitly (precipitation, evaporation, flow in, flow out, seepage out).
-- in the simplest case, the reservoir is entirely within a single subbasin. If there are 2 or more tributaries and the reservoir spans more than one subbasin (where its tributary reaches are joined somewhere "inside" the reservoir), things get a little more complicated. I think most people attach the reservoir to the lowest subbasin and hope there are no obvious big errors. A better solution is to move the tributary outlets to the reservoir boundary manually (delete the ones inside the reservoir and add new ones where the tributary enters the reservoir).
-- Jim