Dear Sung,

synRate is not a normalized quantity, rather a direct model parameter. Also, dS is usually defined as the expected number of synonymous substitutions per synonymous site. You should be able to access these quantities after you have run a codon analysis by selecting Analyses:Results:Syn and Non-syn Trees from the menu.

Also, there is extensive discussion of the relationship between model parameters and dS (and dN) in section 1.4.3 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login including an example of how to use a built-in script to generate dS and dN values.

Cheers,
Sergei