depends on how you are going:

~> aclocal
~> autoconf
~> ./configure --with-pd=/path/to/my/pd
~> make
~> make install

or

~> make CONFIGUREFLAGS="--with-pd=/path/to/my/pd"
~> make install

note that the CONFIGUREFLAGS will have no effect if Make.config is
already up-to-date, because then configure won't be executed. (if you
are working on a "clean" copy of iemmatrix, it should work however)

furthermore, there is a PREFIX in the Makefile (Make.config)

mfg.adsr
IOhannes