I mainly use Qantas FF points for seat upgrades.

I mainly use Qantas FF points for seat upgrades. One thing I have been unable to find out, is, if I book and pay for an Emirates flight to London now, for travel post April '13, will I be able to upgrade my seat at later date if/when the alliance goes ahead ? I'm not sure whether to take the punt and end up being stuck with an economy seat.

I would doubt this very much!

In the Q&A regarding the alliance, it states

"QFF will be able to use points on either network" 

Can I use QFF points on Emirates flights now ? No, the agreement won't take place until the partnership commences in 2013.

But I'm not using points "now". I would be upgrading with points "after" the commencement ofthe partnership. 

I suspect that initially QFF flyers will only be able to upgrade using points on Emirates flights on a QF booked itinerary.

How does it work with other oneworld flights/bookings now?

But it is different here, this is a partnership.

It also states on the Q&A  under "ticketing" 

Customers wil be able to book flights with either carrier, via the Emirates or Qantas web sites

Correct, but I doubt you'll be able to book QF codeshares on EK metal on the Emirates site. I would expect these are the only EK flights you'll be able to upgrade.

I'm 99.9% sure that as per current policy you will only be able to upgrade on a Qantas operated aircraft with a Qantas flight number, so QF1/2 or QF9/10. Upgrades on Emirates operated aircraft highly likely won't be offered.

Agree with @Adam - it's unlikely they are going to let you upgrade on an Emirates flight with Qantas points. Currently you cannot do this with any Qantas codeshares so not sure it would change.