I have TeX files that Aquamacs compiles by default with pdflatex and other files compiled by default with latex (so I get a dvi).
If I make a copy of file that Aquamacs compiles with latex, that copy is compiled with latex. Similarly, a copy of a "pdflatex file" will be compiled with pdflatex.
I can't see where there could be some metadata of my TeX files that could tell Aquamacs with which engine it has to compile.
setq-default TeX-global-PDF-mode t in my .emacs
What determines which compilation is done?