Are you interested in amassing QFF points and QFF SC?
If not, book everything under the EK flight number, ergo earning under Skywards.
If you do want QFF benefits, ie to collect QFF miles and QFF SC, then book under the QF code, which can be a bit pricier.
If you book under the EK flight number, but enter your QFF number, you will earn less QF points and no QF SC.
More info needed.
EK is not in the OW alliance, so you will not get any benefits if you are already a member of a OW alliance airline, and if you fly EK flight number, your OW alliance airline account points won't rise.
If you are interested in collecting OW alliance points, join QFF and put the booking under the QF flight number, you will earn QFF points at the rate as if you were flying a QFF flight number, and QFF SC.