Hello,
You wrote you read the WAQTEL manual reference, you mean the one which describes every keyword like the dictionary with names, default values and helps? Or the WAQTEL Technical Manual (aka WAQTEL theory guide)? This last one describes the variables and equations solved in the WAQTEL modules.
I cannot tell you more than what is written in these two manuals and also the WAQTEL user manual.
The tracers can be managed like every tracer in TELEMAC-3D. Please read the TELEMAC-3D user manual to deal with boundary conditions of tracers or puncual source points for exeample.
Hope this helps,
Chi-Tuan