Do you want to set it for the Eclipse IDE itself, or for the application that you are launching from inside Eclipse?
If it is for the Eclipse IDE itself, then editing eclipse.ini is the way to do it.
For launching programs from Eclipse, see Run > Run Configurations... > Java Application > (project name). On the Arguments tabsheet, put the -Xms and -Xmx switches in the "VM arguments" box.
Program Arguments are what are sent to the main() method of your application (the args array), while VM Arguments are what is given to the JVM (this is where the -Xmx and so on would go)