Yes, only one executer is expected in on custo code deployment. You can put all the functionality in one custom code that you want to call in single method from your app. You can make separate deployment for different app functionality to make it modular.
One Custom code can not make a call to another using runJavaCode method inside custom code. You can make a private method inside your custom code and call it internally though.
Let me know if it makes sense.
Ajay