For this you need to run the "tomcat6w" application that is part of the standard Tomcat distribution in the "bin" directory. E.g. for windows the default is "C:\Program Files\Apache Software Foundation\Tomcat 6.0\bin\tomcat6w.exe". The "tomcat6w" application starts a GUI. If you select the "Java" tab you can enter all Java options.
It is also possible to pass JVM options via the command line to tomcat. For this you need to use the command:
<tomcatexecutable> //US//<tomcatservicename> ++JvmOptions="<JVMoptions>"
where "tomcatexecutable" refers to your tomcat application, "tomcatservicename" is the tomcat service name you are using and "JVMoptions" are your JVM options. For instance:
"tomcat6.exe" //US//tomcat6 ++JvmOptions="-XX:MaxPermSize=128m"