I've always found it difficult to use stitch markers. What I do now when I knit socks is to:
1) Read the pattern fully before starting.
2) Where the pattern tells you the number of stitches to use to start the heel flap - I split those stitches between the first and third needles to begin with. The remainder of the stitches are on needle 2for the instep. Of course this is a preference because I find it a PITA to use 4 needles for socks so I only ever use 3.
3) Then, having arranged the stitches this way, I join the first few stitches knitting with both the working yarn and the long-tail (automatically weaving in the end). Then when I drop the tail yarn it's in (about) the middle of the first needle.
That way you can always keep track of which one is the first needle no matter how far you get on the sock and the beginning of the round is ALWAYS between the needles with the less stitches (top of the triangle, back of the heel...).
Does that make sense? Just my way. I'm sure you'll find something that works for you.