The parameters that control the way that LIGPLOT minimizes a given plot (in terms of reducing the numbers of atom-atom, bond-bond and atom-bond overlaps) are given at the end of the ligplot.par file.
It is unlikely you will need to alter these values, although sometimes you might get a better plot by altering the parameters by trial-and-error.
A far better way of improving a cluttered or unclear plot is by modifying the ligplot.pdb file, as described in section 6.
MINIMIZATION PARAMETERS ----------------------- 0.25 <- Atom-atom clash parameter 0.25 <- Bond-atom clash parameter 10.0 <- Bond-overlap score 1.00 <- Weight for bond-overlap term, relative to atom-clash term 50.0 <- Weight for term giving H-bond deviation from ideal value 7.0 <- Blow-distance for H-bonded groups (in Angstroms) 15.0 <- Furthest move-distance for H-bonded groups (in Angstroms)