Bigger is better (softer) but needs more power and shoot-throughs are quite wasteful of light which is bounced all around the room. But that's why people like them - all the light coming in from ceiling and walls adds extra fill in. Don't use a shoot through outside as the light will just vanish into thin air. I think the smaller one - 36in is still pretty big.
Also, the closer you position the light, the larger it becomes relative to the subject so softer that way, and moving it closer also increases the light output. However, by the same token, light falls of very rapidly at close distance. Inverse square law - double the distance = quarter the light, eg light 3ft from subject gives f/8, 6ft away and you're straight down to f/4.