As with the s2 it will depend on the current firmware, I'm on mdf which rooted
fine with cfroot method, currently I have not flashed a recovery though so cannot backup or flash custom Roms.
I tried looking for a software update through the phone but said I'm not able to so would expect kies to be the same. I've not even had the s4 connected to kies though as I rooted within 2 hrs of getting it.Lol
I do believe you could probably flash the stock pre rooted firmware if you wanted the upgrades or just wait for more custom Roms. Alternatively flash stock updates through Odin and re root!
But I'm pretty sure kies won't be available!