It appears that you have to apply as though you are applying for a job at Emirates and you are screened through the process. As it stands the requirements for Capts and F/O's are the same as Emirates. If you don't meet the mins (8000 hrs with 3000 PIC for Capts) you will get an automated response telling you to apply again when you meet the requirements. Unless they tweak the program where there is some link or place on the app to put in FlyDubai, you are basically completing an Emirates App. I think that they will be tailoring an app for FlyDubai in the near future or screen applicants from the Emirates side.
It will be interesting to see what the pay package and T&C are like. If they are somewhat similar FlyDubai might be a better place to hang your hat. You would be home more often without having to pass through numerous time zones etc etc... Ofcourse no wide-body flying.