The reason for marker beads is rather simple. While meditating the mind often trails off in one of those stories that we tell ourselves and the weaving of a mental tapestry takes us away from the very moment of mantra. So what the marker bead does as it acts as a "wake up call" or a "check" to make sure you are aware of what you are doing.
Once the mind trails off you will continue to count the beads but will "forget" what you are doing because the mind is somewhere else and once you come across this marker bead which is different from the rest it is like a little slap :) to tell you to come back to the mala and your mantra.
Another good use is that you may be reciting the mantra and wondering "AM I THERE YET? HOW MANY MORE BEADS TO THE END?" and once you come across one of these markers you will then know where you are in the count and will then be able to ease the mind again because the agitation of wondering where you are in the mala is over (for the time being :)
We recommend the HUM SA or SO HUM mantra as it is called both meaning "I am That" or "That I am" and you synchronize with your breath - hum on the inhale - sa on the exhale paying close attention to the pace of your breath and trying to equalize both the inhale and exhale. Eventually the space between breaths will become longer - as the space between breaths becomes longer try to focus on this very space.
PLEASE NOTE: In our designs these marker beads are COUNTED except if they are discs. If you want a mala that has markers that are NOT counted please tell us.