Upgrading Windows 8 to 8.1 Pro via Windows Store
I would set Windows to be the default boot until the update is finished, to prevent it being interrupted by unexpectedly booting to Mac.
I don't think it would hurt anything if it did, as the Windows install would simply wait until next time it was booted.

I would definitely update Bootcamp before Windows, in case there is something about the existing drivers that may prevent you booting/finishing/accessing the Windows install if you did it the other way round.

I would, of course, also have a backup of everything before I started.