In model_initialize_real.F or wherever you want the tracers to go, you need to initialize the tracers first as zero everywhere....or you can also initialize them as a certain value.  Both examples are given.  Here is a snippet of the code (just search for tracer or stuff).  Note that tracer_opt is a namelist flag you'll set in the namelist.

!  Our tracer arrray init thingies

      IF ( config_flags%tracer_opt == 1 ) THEN
         DO j=jts,MIN(jde-1,jte)
            DO k=kts,kte
               DO i=its,MIN(ide-1,ite)
                  tracer(i,k,j,P_stuff1) = 0.0 [HERE THE TRACER IS INITIALIZED AS ZERO]
                  tracer(i,k,j,P_stuff2) = 0.0 
               END DO
            END DO
         END DO

         k=kts
         DO j=jts,MIN(jde-1,jte)
            if ( abs(j-jde/2).le.4) then
                jw = 1
            else
                jw = 0
            end if
            DO i=its,MIN(ide-1,ite)
               if ( abs(i-ide/2).le.4) then
                   iw = 1
               else
                   iw = 0
               end if
                 
               val = 1.e-6 * real(iw) * real(jw)
               tracer(i,k,j,P_stuff2) = val [HERE THE TRACER IS SET AS A CERTAIN VALUE]
            END DO
         END DO
      END IF

Next in the namelist, set a namelist value of tracer_opt.  If you have tracers in different domains, you can specify them separately.

In the Registry, find the tracer section.  I've added my own package of tracers called stuff.  I didn't choose the name...Dave Gill, the guy that was helping me chose it and I didn't feel like changing it. :P  You can be more creative if you want.  You need to modify three things in the registry...the names of the tracers you added in module_initialize, the package name, and the namelist option.

[SET THE NAMELIST VALUE IN THE REGISTRY]
rconfig   integer     tracer_opt          namelist,dynamics     max_domains    0       rh    "tracer_opt"  
[MAKE A NEW PACKAGE AND TELL THEM WHICH TRACERS ARE PART OF THE PACKAGE]
package   tracer_prac1  tracer_opt==1       -             tracer:stuff1,stuff2
[NAME THE TRACERS YOU'LL USE IN THE REGISTRY (NOTE, I HAVE 15 TRACERS NOW AND I JUST KEEP ADDING THEM ON HERE AND ABOVE)]
state   real    stuff1     ikjftb  tracer        1         -     irhusdf=(bdy_interp:dt)    "STUFF1"         "Practice tracer #1" -
state   real    stuff2     ikjftb  tracer        1         -     irhusdf=(bdy_interp:dt)    "STUFF2"         "Practice tracer #2" -

Finally, in solve_em.F you need to add your tracer source or whatever you want it to be.  For example, this is a tracer source at 4 grid points in each time step.  At the location (40,1,40) and the 3 points above it, the tracer value is set to a certain value at each time step.  This isn't the best way...its better to add it to the value there.  For example tracer=tracer+source so you don't have a loss of tracer by resetting the value.  But you get the idea.  For some reason its best to use really small value of tracers like e-6 shown here.  I'm not exactly sure why but thats what i was told.  You can always scale it up later.

  IF ( config_flags%tracer_opt == 1 ) THEN
     IF ( grid%id == 1 ) THEN
        tracer(40,1,40,P_stuff1) = 1.e-6 [SMALL NUMER IS IMPORTANT!]
        tracer(40,2,40,P_stuff1) = 1.e-6 [MAY WANT A SUM INSTEAD OF A RESET]
        tracer(40,3,40,P_stuff1) = 1.e-6
        tracer(40,4,40,P_stuff1) = 1.e-6
     END IF
  END IF

Look for these pieces of code in the 4 files attached.  Search for tracer or stuff and you should find em.  I think it is somewhat random where they're placed, but for example in solve_em, the code snippet needs to be in the RK loops.

Modify namelist and registry so the code knows what these tracers are.
Initialize them as zero or as a set value.
Use solve_em to modify them with each time step.