I haven't take care of the translations for quite some time...
For updating the .pot and .po files with the texts in the Java files, if you already have gettext tools installed, you just have to set to true the two variables you have found and commit at the end.
It may be better not to modify the build.xml file (so that other people don't run the i18n part by default), but just add -Ddo.create.pot=true -Ddo.create.po=true to the JVM options of build.xml (in the settings in Eclipse)
Once the .pot and .po files are committed, they are automatically taken into account by launchpad website every 6 hours.
For taking into account translations made by other people, you have to go to launchpad and download the translations (either all of them, or just a few if you know which ones have changed) from https://translations.launchpad.net/jmol/trunk/+translations
You will receive a mail with the link to download the translations.