install patch clm 5.0.2 in websphere

The instructions are the same regardless of WAS or Tomcat version.
To install the server patch:

a. Stop the CLM server.
b. Verify whether the following directory exists: <server_installation_directory>/server/patch.
        -If the directory exists, back up and remove its contents.
        -If the directory does not exist, create it.
c. Copy the server patch file <PatchFile>.zip into the /server/patch directory.
d. Clean the application server cache. Follow your application server's documentation on cache cleaning. Use "To clean the application cache in WebSphere" and "To clean the application cache in Tomcat" below as a reference.
e. Start the CLM server.
Note: For a distributed CLM deployment, complete the same steps on each server.

if my installation directory is / op /

/opt/IBM/WebSphere/AppServer/profiles/AppSrv01/temp/foxtrotNode01/server1/jts.war

the directory where you have to create the patch is in / server?
/opt/IBM/WebSphere/AppServer/profiles/AppSrv01/temp/foxtrotNode01/server1/

You need to look at the JAZZ_HOME location where you installed the CLM products.  The path you have provided is in the WAS profile.
The default location would be /opt/IBM/JazzTeamServer