Dear Dan,
transmission line model of a patch antenna does not give so accurate
results if you are trying to obtain very precise results. So be
careful. It just gives a rough estimation. I have never used RF
toolbox of MATLAB. I am not sure whether or not, you can implement
different feeds to your antenna and different substrate layer
(multilayered structures). You may try Ensemble or HFSS if it is
available in your lab. In these softwares you can try any type of
feeding approach and you can place layers very easily.
Regards,

Kagan TOPALLI
Research Assistant (Ph.D Candidate)
MEMS-VLSI and EMT Group
Middle East Technical University
Dept. of Electrical & Electronics Eng.
TR-06531 Ankara Turkey
Phone: +90 312 210 44 09 or +90 312 210 45 26
Fax: +90 312 210 23 04
http://www.mems.eee.metu.edu.tr/
http://www.eee.metu.edu.tr/~emt/