@James ********
okay there we go, NOW we're getting somewhere
What you really have is a 90 day Non-O visa, then a year extension added to that AND then a multiple re-entry permit
Those are ALL sold separately; the 90 day Non-O visa, the year extension and then finally the multi-re-entry permit.
You're not actually here on ANY visa anymore because that Non-O visa you got when you started the process was only good for 3 months and what you're here on now is actually the stamp that says "EXTENSION OF STAY PERMITTED UNTIL" and has a date a year out.
Seeing as you said you also have a multiple re-entry permit <- which is it's own stamp good until your year extension, you don't need to do ANYTHING when you leave the country. Just show up and stamp out
When you come back into the country you need to turn your passport to the page that has the re-entry permit on it when you hand it to the passport control so they can see you DO have a re-entry permit and they stamp you in for the year stamp you're supposed to have (not on a free 30 day stamp).
When they give the passport back check the small red entry stamp and make sure it says Non-RE on the top and has a stamp the same expiration date as your extension/re-entry permit