RT 3.6.3 - running two instances on the same box

Now that i have to instances of RT up - i have yet another question: when
installing extensions, sometimes, i can’t get the install to point to the
second RT instance. I’ve tried doing the ‘RTHOME=/path/to/second/instance
perl Makefile.PL’ but some extensions still only point to the first one. How
do i work around that? Change the Makefile manually and then run the make?
Thanks in advance,