Buring 40k miles ex Aus
 

I have 40,000 points expriring end of Jan

I am based in Australia.

My plan was to buy a cheap Y fare SYD-AKL/CHC and use the points to upgrade.

Is there any way of checking whether this will be possible to do before buying the tickets?

yes
log into your account on Emirates website (not skywards)
Then do a search for miles redemption for the dates you're after; if it shows availability in Business (not Peak Business) you're generally on the safe side.

You can also call skywards, they're quite helpful.

Or you can go to http://publicbackup.com/shared/flyertalk/availability/ and look flights there, if you see availability in I fare bucket then you're on the safer side but this one is not guaranteed; because I have upgraded for family members several times even though when C was zeroed (back when it was C) and I was zeroed.

How is doing it through the Emirates site different to Skywards? I always check this through skywards site.

The skywards site only lets you see your current miles etc. I don't think you can actually make EK bookings on that. To do so you need to log into your account on EK and make a booking.

From http://www.skywards.com/travelonlineBooking.aspx you will be redirected to EK website.

Oh cool - I never realized that was possible.

EVen if you use the skywards site, it will re direct you to emirates site and you may have to log on again. If you have a emirates/skywards office in your country/city you can also call them and ask them if they have seats for upgrade on that particular flight, usually they are very helpful.