Each type of ballistic weapon looks different on the JM, and that's ace. Keep in mind that whichever cannon you equip first will go on top, so make sure to add them in the same order on each side. Otherwise they'll end up opposite. I think it makes the mech look like it's leaning, and it drove me mad the one match I had to suffer through it. You have been warned!
I'm pretty sure it is. I will do this on my Stalker - put my ER PPCs or ER LLs on first, and then put my MLs on after, so I'm getting the highest platform for my sniper weapons.
I just did it with the JM6-S by putting an AC/2 and an AC/10 in the arms and it always puts the AC10 on the bottom and the AC2 on the top.