HTML:

<ya-map ya-zoom="10" ya-center="[37.75,55.73]">
    <ya-collection ya-options="{preset: 'islands#yellowIcon'}">
        <ya-geo-object ng-repeat="o in oneObjects" ya-source="o"></ya-geo-object>
    </ya-collection>
    <ya-collection ya-options="{preset: 'islands#blueIcon'}">
        <ya-geo-object ng-repeat="o in twoObjects" ya-source="o"></ya-geo-object>
    </ya-collection>
</ya-map>
    

javascript:

$scope.oneObjects = [
        {
            geometry: {
                type: 'Point',
                coordinates: [37.75, 55.73]
            }
        },
        {
            geometry: {
                type: 'Point',
                coordinates: [37.75, 55.81]
            }
        }
    ];
    $scope.twoObjects=[
        {
            geometry: {
                type: 'Point',
                coordinates: [37.65, 55.73]
            }
        },
        {
            geometry: {
                type: 'Point',
                coordinates: [37.65,55.81]
            }
        }
    ];