If you have configured your subprocess pool correctly and licensing is in place then your publishing should be working. Have you checked the PE (E3) status page and tried the test links?
Thank you for your reply, I managed to resolve it by changing to local system in Logon in tomcat configuration. However, we encountered another error when calling an activation file - 'Fata Error running ALD library'. Do you have any idea what does this mean?
Yes local system account is easiest if that is feasible. There may be some concerns based on your organisation's security policies and if so you can run Tomcat as a more restrictive user account but that obviously needs extra configuration such that the Tomcat user has correct privileges.
For the ALD library issue you might want to raise a PTC support ticket. They supply an APP-E compatibility library that does the hard work of translating APP-E activation files into what is needed by PE. Therefore they should be able to support their library and ensure you can at least get a test job working.
Alternatively there are third party services providers such as our company (www.gpsl.co) that are able to assist, that would be on commercial terms though. We still retain some staff from the original Arbortext and APP/3B2 companies.