I use Tomcat 6.0 and Eclipse 3.0 under Linux and I try to deploy a WAR in Tomcat. The problem is that the server is managed by Eclipse and I have some Eclipse project deployed.
This is old but is one of the first answers in google search.
You can import the war file:
A Web Archive (WAR) file is a portable, packaged Web application that you can import into your workspace.
Before importing a WAR file, you should first determine if the WAR file contains needed Java™ source files. When importing a WAR file into an existing Web project, the imported Web deployment descriptor files are either not changed or overwritten by the ones included in the imported WAR file, based on your response to the prompt that is provided. In either case, this action does not represent a merging of the two sets of deployment descriptors.
To import the Web project resources in a WAR file into your workspace, complete the following steps:
Source: http://help.eclipse.org/luna/index.jsp?topic=%2Forg.eclipse.wst.webtools.doc.user%2Ftopics%2Ftwimpwar.html