People applying with occupations on the CSL while it still exists will have relevant priority applied.
Immi in announcing changes to progressively take place has indicated there will be transitional arrangements that are yet to be announced and I'd suspect they will be developed in accordance with the new State Migration Plans, eg. [ my guess ]
I would expect that most CSL occupations might well appear on SMPs and as such a couple of different approaches could be adopted:
. Existing regime of CSL priorities is continued in conjunction with SMPs with both an SMP occupation and a CSL occupation with state sponsorship having priority #2 and those without state sponsorship having the option for sponsorship via SMPs if higher priority is sought.
. CSL occupations not appearing on any SMPs will have the lower priority as they do now if without state sponsorship.