If you are not going to use it right away, certainly.
I've not tried homemade, I've only used organic yogurt. (It's difficult to find plain yogurt!)
My method is to heat a solution of half yogurt and half whole milk slowly on the stove, stirring with a wisk to breakup the yogurt then quickly transfer to the enema bag.
Since this is a rather thick solution, the bag must be hung higher than normal to get the solution to flow. A retention nozzle, one with large openings, is a must.