Ammo in the head is there because it is near impossible for it to explode, your head has 15 internal structure, and ammo has 10 health plus there are 5 other critical slots (filled with cockpit and life support type things) to spread the critical damage.) So before it explodes your head will be vaporized anyway. The second place you should put Ammo is either your legs, or an arm that is difficult to hit (cicada, jaggermech, blackjack) Really just play 20+ games and find what part of your mech almost never gets destroyed and put your ammo there.
On the Stalker in general I cannot recommend you using it as a first mech. The problem is it has a very very horrible turning speed. This may not sound that bad, but at Low to medium ELO you have lots of decent light pilots that will be able to stay behind you no matter how you turn. Once you get all your elite skills (this doubles all basic skill effects) then this is no longer a huge issue, this requires you to have 3 Stalkers though. At higher skill level your teammates will be better at assisting you on lights, and fewer enemies will be in lights since they get killed more easily at those skill levels, so the stalker is a better mech there.
As to the 5S specifically if you are going to use it put on 2xAMS otherwise use the 3-F (this can rotate its torso further)
on your first build I would change it to this
STK-5S however I cannot recommend the stalker as a pure missile boat, it just has too many problems like tube counts and unless you fit in your 6ML has no advantages.
on your second build I would go:
STK-5S until you get your elite skill to get the added heat dissipation I think that the 2 ER + 2 PPC will run too hot for you, if you do go with it put both ERPPC on a single arm for firing around corners. I would not go with streaks because you will find you cannot turn fast enough to keep a lock on a light mech, That said going with all 4 being streaks might scare better light pilots so they never engage you, but a mixed SSRM/SRM loadout tends to not work well, go with one or the other.
IF you want to go with a Stalker what I would suggest is:
STK-5M 5xLRM5, 3xERPPC Although again switching to a 250ish standard engine may be preferable, it depends on how much the added speed helps you, because you do lose some survivability.