Hello sobo634,
As already told by Sébastien, the use of TELEMAC-3D rather than TELEMAC-2D (or conversely) depends on what type of tracer you have. Is it a passive or an active tracer (i.e. does the tracer have an action on the hydrodynamics, e.g. the law of density depends on salinity or temperature and these two tracers should be better modelled with TELEMAC-3D). Moreover, as Sébastien told you, if you have any buoyancy effects, you should use TELEMAC-3D. This software is not so difficult to use compared to TELEMAC-2D and not so different.
What is your tracer? Is it a simple pollutant that is only transported by water?
If it is a passive tracer and you do not mind to see any vertical distribution (and you do not have any buoyancy effects), you can use TELEMAC-2D (but in all cases you can always use TELEMAC-2D, but results really depend of the nature of your tracer).
At last, I would suggest you to read the different manuals available in Home section, then Manuals.
Hope this helps,
Chi-Tuan