Can I have multiple instances of PHPEmbed in one program?

Yes, this version of PHPEmbed can support multiple PHP objects in a single binary if it is compiled with Zend Thread Safety (ZTS) enabled. This is still experimental so there may be bugs, especially around memory usage, but each object operates in its own memory so they can be used concurrently. If the access to the PHP object is relatively sparse it may be worth using a single PHP object and passing it to multiple threads.