Unless I'm misreading it, the pattern says not to work them. This is the section that I'm at:
K1 round, P1 round in contrast color
K1 round, P1 round in main color
Repeat pattern 3 (3,3,4) times. 30 (30,32,36) total rows.
For size 6mo. K1 round, P1 round in contrast color. 32 rows total
Leave yarn at back of work. You will pick up here later.
Slip next 10 (11,12,13) st. onto spare needle. Do not K these st.
On RS K next 10(11,12, 13) st. in color that continues pattern.
(color may differ depending on which size you are making)
Turn. On WS K 10 (11,12,13) st. in same color.
Repeat pattern until 18 (20,22,24) rows are completed.
I'm afraid I don't really know what you mean by "the new end". Do you mean I could start the Instep with a new yarn that hasn't been attached to the garment (i.e. that won't be connected to the old yarn)? If that's the case, then I don't really know why it says to slip any stitches since those 12 stitches that it says to slip are already on their own needle, I could just skip over them.