Adding and showing markers on Tomtom map without using clear() function using this simple logic. Create a boolean variable and change it according to your needs. Buttons will do, just switch the values from true to false or false to true to display.
MarkerBuilder marker = new MarkerBuilder(LatLng)
.icon(Icon.Factory.fromResources(MainActivity.this, R.drawable.markerIcon))
.tag("marker-name");
if(putMarker == true) {
tomtomMap.addMarker(marker);
} else {
tomtomMap.removeMarkerByTag("marker-name");
}