Are you knitting top down or toe up? For toe up you start the gusset shaping 2-3" before the sock is at the back of the heel, depending on what kind of heel you are doing. For top down you start the heel flap (its the only heel I have tried with top down) when the sock is at the desired legnth then do the heel turn and then begin the gusset shaping. Does this help?
Are you doing top down socks? Are you using the magic loop? or 2 circs? My directions are for the magic loop, but I'm sure it would be similar with 2 circs.
Here are top down socks on dpns.
Here are the same socks on ML.
The top dpn and the cable have the instep stitches on them.
The dpn on the left and the cable needle on the left are the beginning of the round. The dpn on the right and the cable needle on the right are the end of the round. These are the back of the sock and the sts used for the heel flap and gusset. The heel flap with be worked using all the back sts. Then you will turn the heel.
So once the heel is turned and you pick up sts for the gusset, these sts will be in the same position as the back sts are in these photos. Part of the sts will be from the turned heel and part will the sts you pick up to form the gusset. Be sure to use a st marker to mark the beginning of the round.