Heat sink on the bottom or on the side?
An orientation that puts the cooling fins vertical will give a better cooling effect if the airflow is not forced (by a fan). 

Hot air rises so you get better airflow over the fins if they are arranged vertically,

If the airflow is forced  you will get better airflow if the fins are aligned with the direction of movement of the air. 

Due to the thermal conductivity of the heatsink there will be very little difference in the vertical or horizontal positioning of components relative to the heatsink position.