I'd need more explanation of the problems to advise.  In your command "sym #3 h,1.6,118,30,-10 center 120,120,120" the 30 is the number of repeats of model #3 in the helical assembly.  You can of course increase that number to make a longer stretch of helix.  I'm not sure what you mean by "several layers".   If the assembly is not centered on your map there are various solutions.   For helical symmetry maps I think the best approach is to make the symmetry axis the z axis and passing through the origin 0,0,0.  You may need to shift the origin index of the map (ChimeraX menu Tools / Volume Data / Map Coordinates).  This defines the grid index of the map that is supposed to have x,y,z = 0,0,0.  If your map is 240 by 240 by 240 in size the center of symmetry might be at 119,119,119 or 120,120,120 (the two points close to the center of the box).  You can save a new .mrc file for the map to remember that center.  In addition to get the sym command to produce a helical atomic model that fits you would start with one copy of your asymmetric model fit into the map, then use the sym command on it.

  Docs for sym command

  Tom