You need to put the bolt upwards through the lower arm and subframe with the nut on the top.

It will make it a bit more awkward to do up and undo but this is fuck all compared to exposing the remainder of the thread to all the water, dirt, salt and shit that gets kicked up to the underside of your car. Leave those threads exposed and you will NEVER get them undone again once the threads corrode away!

All bolt heads should be at the front or on the bottom with exposed threads pointing towards the back or top of the car to give them maximum protection against the elements!