You can put the WAR wherever you want. Some places are, of course, better than others. The main constraint is that the directory that serves to contain the WAR has to be readable by Tomcat.
Tomcat has a "webapps" directory and most people use that, since they don't have to setup context information and it's a common, well-known place to hold WARs. My serious apps treat WARs as independent products, which have their own product directories and the WARs live there, instead. I use a TOMCAT_HOME/conf/Calatlina/localhost/xxxxx.xml Context file that points to that WAR using the appBase attribute.
There are roughly about 7 places and ways to deploy WARs, and that's not even including the alternatives such as using the Tomcat Manager webapp to upload and install the WAR.
An IDE is no substitute for an Intelligent Developer.