The simplest method to customise texi2latex's result is to create a file mymanual-t2l.cfg in the same directory as mymanual.texi. It is read by LaTeX when the document is processed, and it is interpreted as last part of the LaTeX preamble. Thus, it should contain LaTeX preamble macros that affect the global layout. For example,
sets Times as the default font, Helvetica for sans-serif excerpts, and Courier for fixed-width excerpts. For further information, consult any good LaTeX book or manual.
If a file called texi2latex.cfg is in a search path of TeX (including the current directory), this is interpreted like the document-specific configuration file from above. It has lower precedence though, i.e. any re-definitions in the document-specific file override the global one.
This global config file contains settings for all texi2latex runs. It's a good place for page size and margins settings, but there's no reason not to include font definition commands as well.