Just make sure to space the forward air properly, especially if you're coming from above.
If you don't space correctly, you'll have a high chance of meeting with the Cipher too early and you'll collide with it. If you get hit by the Cipher, it will hit you (obviously), but the important thing to remember is that when you get hit, the attack you were winding up when you get hit stops. In short, if you space wrong or start the forward air too late, Cipher will stop the move, Snake will keep rising, you won't have enough time to forward air again, and Snake will most likely take care of your double jump with a back air.
That being said, try to forward air from the sides or the bottom, if at all possible. You can still do it from the top, but the spacing and timing are quite hard to pin down if you're not used to the new forward air timing and spacing yet. I know it took me a good two weeks to get hitting Snake down, not even counting getting the timing for the new move down.
On this note, if you manage to forward air Snake out of his Cipher, grab the ledge and
do not let go. You should only really let go under the following circumstances: 1] Snake lets go of his Cipher and has no conceivable way of reaching the ledge (mostly form below) and you see that the Cipher will hit you, 2] Snake's Cipher recovery will allow him to get not only to the ledge, but also onto the stage--Yoshi's off-the-ledge game is not good at all (yet) and you don't want to risk too much, 3] Snake's Cipher will
almost juuuuuuust barely get him to the ledge but he still won't grab it--you don't want to be in this position...even though Snake will fall, he still has two options...he can perform an up air, which will likely take you out with him (unless you've learned to tech, which is unforgivably hard), or he can use his C4 explosives to boost himself up to the stage (which can knock you off-balance with dead weight and then he can proceed to perform safe high-priority aerials while falling).
I know the above sounds extremely arbitrary and a little confusing, but you should just use your best judgment. Don't let go unless you'll get KO'd or Snake has no chance of getting back
period.