I had the same task. I had to model a stream which had a bypass channel running parallel to the stream approx 100 feet away. I had to model two culverts, one in the main channel, and one in the bypass. First I tried to model it with two streams and split flow optimization, but i lacked sufficient survey information to develop accurate upstream and downstream cross section. I then noticed that the ground surface elevation between the two streams is less than the high water for the storm profiles i was designing for. So it seems like it was more appropriate to do one wide stream with two stream openings and two culverts. Fortunately i had enough survey information near the culverts to develop a local very wide model of the two streams together.
This is just my situation. The only advice i can offer is to consider treating it as one large stream if they are close and the ground surface elevation between them is lower than your water surface elevation.
I’ve got the split flow model if you want to take a look, however i can’t claim it is even close to accurate or correct due to the lack of survey data.