This is how its normally done in the init.sqs
?side player==east:"WStart" setmarkertype "empty"
?side player==east:"Respawn_West" setmarkersize[0,0]
If its an icon set it to empty
if its an ellipse or rectangle set its size to 0,0
On the fly ??, dont know, but what you could do is basically create all the markers you want during mission editing, initially have them unseen, then when you want, set their positions to wherever you want them, set their color size type etc
here are the marker commands avail
"mymarker" setmarkersize [x, y]
"mymarker" setmarkerpos getmarkerpos "myothermarker"
"mymarker" setmarkercolor [colorblue]
"mymarker" setmarkertype "Destroy" (see comref for others)
other colors are "colorredalpha", "colorgreen", "default" and others see the command ref