Are you sure the 9" needle is long enough to easily and comfortably accommodate the gusset increases? I use stitch markers if I need to define specific parts of a pattern on the needles. If I use a pattern for dpn and do magic loop I use markers to indicate needle 1, needle 2, needle 3 if I need to know the stitch distribution.
The OP stated in her heading that she is knitting the Fish Lips Kiss heel which does not require (although it can be done) gusset increases. If she wants to use the template (part of the FLK heel method) why switch from magic loop to 9" circulars? or switch after the heel is completed.