Hello Mathilde,
Normally, if you correctly fill in the SOURCES FILE (in particular with Q(...) values in the headline, as many as the number of sources determined by the size of the WATER DISCHARGE OF SOURCES keyword), you can give dummy values to WATER DISCHARGE OF SOURCES and it should work.
Minus sign for water discharge means water is exiting the domain (OK with an intake, not a release).
For intakes, I am not sure that giving values to VELOCITIES OF THE SOURCES ALONG... keywords is a good idea, I would start not giving any information to those keywords.
Depending on if you model tracers or not and if there is information in the SOURCES FILE, you may need or not to fill the VALUE OF THE TRACERS AT THE SOURCES keyword.
Hope this helps,
Chi-Tuan