I have two Web Apps (two war-files) in WebSphere. As I understand I can configure the thread pool under:
Servers > Server Types > WebSphere application servers > server_name > Thread pools
Are the two apps sharing the thread pool? If yes, is it possible the have dedicated thread pool for each app?
Unfortunately to use separate web container thread pools in separate applications requires defining separate "transport chains" that terminate in different listening TCP ports (this will normally mean defining a new TCP listening port for http and httpsd).
The multiple sets of TCP ports can then cause some complexity on any frontend proxy.
Fortunately, WebSphere Commerce has some good documentation on it here that is largely applicable to any application:
This takes you through the individual steps of creating the additional thread pool, additional transport chain, then tieing them and the application together.