You can choose to run the signal through the subs to the tops because that's the easiest and most consistent way to get the signal to both sets of boxes. You won't forget to adjust the level of the subs when you adjust the level of the tops. (seen it happen way too often) If you mix your instruments with subs on an aux, that's an obvious requirement for aux-fed subs.
Here is a handy infographic showing a recommended setup for DJs who primarily control their setup through a DJ mixer, and through a mixing board. Live sound engineers should follow standard gain structure rules through their mixing console.