Hope this helps. M marker 2.png shows the position of the chapter marker at the bottom of timeline.
I can change it to a chapter marker beneath the TL and that functions normally.
M marker 2.png shows a standard marker below TL.
I can delete it and try to create a new one but it always goes to the bottom of the TL.
I have 10 other chapter markers in this timeline that all insert above the TL.
Frustrated by this too. Markers in primary storyline and when I create a new one it dumps it to secondary storyline or any other location above SL. Bothers me something fierce when that happens. Likely I'm expecting things to be done logically and not be done the way FCP coders feel they should be done.
Markers always are shown at the top edge of a clip. You have a primary storyline and secondary/connected clips/storylines.
If you add a marker where there is a connected clip or connected/secondary storyline, the marker will be added to the top-most connected clip or connected/secondary storyline. That is, the top-most clip in the timeline gets the marker by default.
To add a marker to the primary storyline when there are clips connected above it, you need to select the clip in the primary storyline and then add a marker.
An example using keyboard shortcuts (with audio skimming turned off):
With your playhead positioned where you want to add a marker, you can use command-up arrow or command-down arrow to choose the specific clip to which you'd like to attach a marker. Repeated use of the shortcut will move you up and down through all the clips that intersect the playhead. If skimming is turned on, markers get added where the skimmer is located.
Another way to place the marker on the exact clip you want is to place the playhead where you want the marker to be located, then move the cursor over the clip and type "C" to select the clip, then "M" (of course) to add the marker. This works with the skimmer turned off.
With the skimmer active, the marker gets placed where your cursor is located, so this option is a bit trickier. Move cursor/skimmer to position where you want to add a marker, then type "C" to select the clip and "M" to add the marker. It may be tricky to not have the cursor/skimmer move before you add the marker. If so, the previous options may work better for you.
This stuff can be a bit confusing and is related to how FCP "auto-selects" connected clips/storylines for varioius operations.