Are you based in the UK? What class are you booked in? Are the Emirates flights QF codeshares or EK flight numbers?
The BA and Qantas flights you can credit to any OneWorld partner, so BA or QF or AA.. However, if it is booked in discount economy, the QF flights credited to BA would only earn 0.25 avios per mile.
Emirates is not part of OneWorld, however they are a Qantas partner. So you can credit those flights to either Emirates Skywards or Qantas. If Qantas, you can redeem for any OneWorld partner award flight.
what happens if you did not do this, flew EK and credited to Skywards, are those miles lost forever (unless one flighs EK again?)