Manual hooping is generally better than automatic, but it does require greater understanding of both design and production processes.
An experienced embroiderer will generally be better able to weigh up alternatives than a purely rule-based software algorithm. This is especially so when it comes to splitting objects between different hoopings. Also, you may have definite ideas about how best to position hoops to make it easier to place fabric and reduce registration errors.
Tip Manual hooping is also better when working with ‘recognized’ machine files.