Hi,
I think it's enought to use control structure. In fact, if you define the struture also as culert, you will end up with to independent culverts, one with gate and another one with free flow. Thus, this second approach is wrong.
If you think the culvert is too long and you want to use a branch to schematize it, you have two options:
1. If entire flow passes throw this culvert, than use two close cross-sections on your branch at the start and at the begining of the culvert. Set up a control structure between this cross sections to control the discharges;
2. Use a separate branche delimitated by close cross-sections. On this branch you can place a control structure.
Good luck!
Aurelian