don't worry about sanitizing in shifts. they will stay reasonably sanitary for a while. If you want extra assurance you could cover the opening of each bottle with sanitized foil until they are all done.
I like to sterilize my bottles in the oven the night before. I stack as many bottles as will fit, or as many as I need anyway, in the cold oven and then turn it on to 350. once it hits temp I let it ride for 20min-1 hour then turn the oven off and walk away. I bottle the next day and just pull the bottles right out of the oven 6 at a time. again, if you want you can put a bit of foil over the opening of each bottle before baking and then they will be all sealed and sterile inside when you fill them.