Great question!  I would say if you expect flows to rise in the main channel, over top the structure and flow up the tributary, then model it as a lateral structure off the main channel.  Otherwise, use an inline structure.  Keep in mind, that if you use an inline structure, you’ll have to have at least 2 cross sections downstream of the inline structure before the junction.  
Even better, try both and let us all know which works better!
Good luck-
Chris
@RASModel