To be honest, Spooner, it's best to do it the way the OP mentioned (as suggested by Kronzky), as then it remains 'compatible' for non-dedicated hosts, too, rather than the host seeing the markers.
The following works perfectly for me in a number of missions:
if (isServer) then {
"patrolMarker" setMarkerPos [-(getMarkerPos "patrolMarker" select 0),-(getMarkerPos "patrolMarker" select 1)];
};
This can be inserted anywhere in the init.sqf. Just add more lines for more markers.