I am using IntelliJ IDEA 15.0.3, Tomcat 8.0.15 and JDK 1.8.0_31
This is an excerpt from C:\Program Files (x86)\JetBrains\IntelliJ IDEA 15.0.2\bin\idea.properties:
idea.system.path=D:/dev/IntelliJ-Settings/system
In Fileβ Settings...β Build, Execution, Deploymentβ Application ServersI defined this: (look Tomcat base directory)

D:\catalina-base-idea Contains Tomcat's global configuration for IntelliJ.
When I deploy my webapp using the IntelliJ launch configuration, the web application will be deployed to D:\dev\IntelliJ-Settings\system\tomcat(see idea.properties).
The above question 1.
Question 2: afaik, targetused only for creation, not for deployment.
Question 3: there is no application manager in D:\dev\IntelliJ-Settings\system\tomcat\webapps
Question 4: magazines are within D:\dev\IntelliJ-Settings\system\tomcat\webapps\yourApp. The global configuration of Tomcat is located at D:\catalina-base-idea.
Tomcat IntelliJ , , 8080. , Tomcat IntelliJ Tomact.