Hello
The use of Tube is recommended for locations where the flow can switch from a free surface one to a close-conduit flow. The flow is approximated coarsely as flow in a cylindric conduit. That's why, you can observe big differences between real flow and simulated one especially if the tube is very long.
To answer to your question: the tube is only between 2 points. Actually, you can introduce more than one tube, in parallel configuration (to simulate greater discharges) by connecting two (or more) close points to two (or more) ohter points in order to have several parallel tubes.
For your case, in order to be more accurate, if you are sure a priori that your flow (in the underground part) will stay always a free surface flow, it is better, in my opinion, to introduce the real shape and bathymetry of the channel and to simulate the case as if it was an open-air channel.
whith my best regards
Riadh ATA