Perhaps start phalcon 1.3 and 2.0 on the same server VDS?
ngnix + php-fpm
you have to be running diffrent php version per host ( like I do )
so your koko.com will be runing /myphp/php-5613/ and your toto.com will be running /myphp/php-5613-with-phalcon-1.3 ( as an exmaple )
a tip can be fond here : https://forum.phalcon.io/discussion/582/php-5-3-3-and-php-5-4-13-dual-installation-error
cd cphalcon/build/64bits make clean phpize --clean /opt/rh/php5.4/usr/bin/phpize ./configure --with-php-config=/opt/rh/php5.4/usr/bin/php-config make && sudo make install