There is a chance that despite your best efforts you might get some separation occurring. You can just stir it in and pop the jar back in the fridge. Often that's enough to get it to stay nicely homogenized.  If there's a lot of separation you have 2 options: Scoop off the creamy top and put it in a clean jar and discard the watery part.  Strain it. Line a sieve with cheesecloth and sit it over a bowl. Pour in the yogurt and cover the top with a clean, fluff-free cloth or more cheese cloth. Place the whole thing in the fridge for 24 hours. The liquid will slowly drip down and out into the bowl leaving you thick and creamy yogurt in the sieve. Once 24 hours have passed, scoop the creamy yogurt into a lidded jar.