I design my quilts and sleeping bags with two main baffle orientations; vertical with a horizontal footbox and full horizontal.

For my quilts I only offer vertical with the horizontal footbox, this is because its the easiest for me to make aswell as many people prefer this baffle orientation as they believe it stops down from shifting to the sides. This is the most highly regarded baffle orientation as there is very little room for down migration. However one disadvantage is that down cannot be moved to the top in colder weather like you can with horizontal baffles. 

Horizontal baffles allow the ability to move the down to the top or sides so that there is maximum loft directly above them where it is needed the most, while limiting the fill along the back/sides where it is only needed to fill the gaps between the sleeper’s body and the sleeping pad

For information on Differential Cut and Overstuff