synonymous/nonsynonymous mutation rate (Ks/Kn)

(1) Ks saturation (Ks > 1):

http://biostar.stackexchange.com/questions/13501/ks-saturation-after-a-pairwise-comparison-analysis-using-codeml

http://sysbio.oxfordjournals.org/content/57/3/367.full
It has been widely accepted that synonymous substitutions may saturate quickly as sequences diverge (e.g., Maynard Smith and Smith, 1996). The analysis of mammal and yeast data reveals that synonymous substitutions are very important and should not be ignored.

(2) intraspecific

(2.1) if you have intraspecific polymorphism data, you should be calculating pi or theta (not Ka or Ks) for synonymous and non-synonymous sites.

http://biostar.stackexchange.com/questions/12153/ka-ks-ratio-to-detect-selection-nonsynonmous-to-synonymous-in-dnasp

(2.2) Within populations or species, there are suggestions that ka/ks may not be a good measure of selective constraints because the selection and ka/ks ratio doesn't follow a monotonic function. See http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000304 from the Plotkin lab. If I were to use ka/ks here, I'll try codon-based approach implemented in HyPhy to see site and lineage specific dN/dS ratio. Also, I think it might be a better idea to explore population genetics based approach, like Tajima's D, to test the null hypothesis of neutral evolution.
To answer your direct questions, yes, you input all coding sequences, and you do get average values from all pairwise comparisons. But I wonder whether you'll see any significant values because they should be all highly similar.

http://biostar.stackexchange.com/questions/12174/ka-ks-ratio-for-within-a-gene-very-confused

(3) new models on mutation and selection

(3.1) Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences

http://sysbio.oxfordjournals.org/content/early/2009/06/29/sysbio.syp015.full

(3.2) Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
http://www.pnas.org/content/107/10/4629.full

(4) The Population Genetics of dN/dS

http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000304