This is slightly tricky to handle with Plesk as the control panel likes to be in control of the Apache configuration files and certain files are automatically generated by Plesk to ensure that system settings remain consistent.
There are a number of approaches you could take depending on your requirements.
1) Make your app setup new sites on the local machine using the Plesk API. This would give you full control of the sites with the control panel and everything that entails. It's also the most complicated solution.
2) If the sites can be addressed with the same domain, i.e. you are setting up subdomains a simple wildcard entry in the conf/vhost.conf for the master domain record would do it:
ServerAlias *.mydomain.com
You could then use this file to also associate other domains with the master domain by writing to it (carefully!) with your app.
3) Setup and configure the Apache module mod_vhost_alias - although Plesk is likely to cause you a headache with this approach.