EDIT: I wrote up my answer and then saw the other one so I wanted to add, before I get into the details - I think this pattern is assuming you have stitches on 3 needles and are knitting with the 4th. If that's the case, then it's right, because the 3rd needle and the 1st needle are next to each other and those stitches will be too. (If you lose track of which needle is which just look for the yarn tail; it will always be at the beginning of the first needle.)
If on the other hand you have stitches on 4 needles and are knitting with a 5th, then there is something wrong with the pattern; you need the stitches on the heel flap to be together so you should put the last stitches on the 4th needle with the first stitches on the 1st. But most sock patterns, at least in the US, assume people knit socks using a total of 4 needles. In Europe they tend to use 5.
If this isn't what you're asking - if you're just trying to figure out how the yarn will end up in the right place later on - I'm going to leave the rest of my answer here in case it helps. If you don't need it then feel free to ignore it. It's below the line.
It sounds like you're making the stocking from the leg down (rather than the toe up) with a "standard" heel, and if that's the case, then no, your yarn won't end up in the wrong place.
To make the heel flap you have to knit back and forth for a while, and usually you do that on only half the stitches; for this stocking that might be a different number, but the key is to work only *some* of the stitches. (The others just sit there on whatever needles you put them on. They might be in the way at first but as the flap gets longer they won't be.) When the heel flap is as long as it's supposed to be then you turn the heel.
Once the heel is turned you should be at the end of a right-side row (if you're not then just add another row; this is a Christmas stocking so it won't make that much difference). *Then* use an empty needle to start picking up stitches on one side of the heel flap; this is the beginning of the instep gusset. (Don't try to use the needle you just used for the heel flap; it won't turn that far sideways.)
After you've picked up all the stitches on that side of the flap you'll be back at the stitches that have been sitting there all this time. You knit across those and then pick up stitches on the *other* side of the heel flap (for the other gusset). Now you're back to working in the round, with no yarn to break or reattach. It's actually a really neat way to do it.
You may have to rearrange the stitches on your needles so you don't have too many on some and not enough on others. And you'll probably have to do some decreasing in the corners of each gusset to get back to the original number of stitches (on a regular sock that's always the case). But after that you should be OK.
Without the pattern to look at I'm making some guesses here; this is a Christmas stocking and not a regular sock. But if it's made like a regular sock that's what you'd do. If not then I hope I haven't confused things too much.
To make a long story short here are the parts you work:
1) heel flap
3) 1st instep gusset
4) foot stitches
5) 2nd instep gusset
And around and around and around until you get to the toe.
I do think this is a great way to learn how to make socks, because a Christmas stocking is so much bigger; it'll be easier to see what you're doing. When I decided I wanted to learn I did something similar; I used Elizabeth Zimmermann's pattern for moccasin socks. They ended up being way too big for my feet (I gave them away), but they were a great way to learn. And after that I was fine. I don't even use patterns anymore.
I hope that helps. Good luck with your stocking.
Lots and lots of knitting experience in general and sock-knitting in particular