The top terminals of the disconnect are meant for the line-side terminals, and the bottom terminals are meant for the load-side terminals. That is the industry norm for how these devices are built. The circuit that remains energized after the disconnect is opened, is what is supposed to be connected on top. That way, the blades, fuses, and unshielded terminals get de-energized when the disconnect is switched to the off/open position. The intent is that as much of the disconnect is de-energized as possible, when opened.
If the geometry of how you are routing your circuits makes it more convenient to connect the line-side raceway to the bottom, and the load-side raceway to the top, it is perfectly acceptable for both circuits to cross over one another in the wiring space, so they can both U-turn to their correct terminals. Even if the line-side conductors classify as service conductors. It is in a raceway or other wiring method, where you are not allowed to mix service conductors and load-side feeder conductors, in order to mitigate the risk of faults. The 1 to 2 feet of shared wiring space in a disconnect is considered negligible enough for this not to be an issue.