It should go above the top fly, preferably just above the lowest tippet knot. That puts the flies down near the bottom where they should be, but has the disadvantage of losing both flies if the s/s gets hung up in rocks.

BUT ...

If you're still using split shot (or twist-on lead), you're doing several things you don't have to do, such as chipping your front teeth, cutting your fingers, weakening your leader, polluting the water, constantly adjusting your weigh to get it to stay in place, and, as mentioned, losing flies needlessly. Honestly, go try the soft, non-lead putty material. Flatten a small amount and roll it on the (dry) leader or tippet anywhere, tapering it and getting it to adhere well. You can add or subtract material easily, it doesn't require a knot to stay in place all day even on 5X, if it gets stuck between rocks you just pull slowly and it deforms and comes free, and a small $6 package will last several years b/c you can remove it and put it back in the package ad it re-blends like Play-Doh. I use something called Sticky-Weight; it's not made anymore, but you may find some on EBay. Loon and others now make it, tho, and it's easy to find.
Try it once and you'll never go back to split shot.