Okay so I finished it all up... here it is if anyone ever wants it. Also, is this an absolutely horrible way to do this? Just wondering since I don't have much of a clue still when it comes to proper practices with JavaScript.(also it doesn't look too pretty right now just because of how I made the map)
JavaScript
<script type="text/javascript">
        function initialize() {
            var mapOptions = {
                zoom: 4,
                center: new google.maps.LatLng(40.866711, -101.465781)
            }
            var map = new google.maps.Map(document.getElementById('map-canvas'), mapOptions);
            setContactMarkers(map, redMarkers);
            setWorkerCompMarkers(map, yellowMarkers);
        }
        var redMarkers = [[39.9406864, -77.8082025],[33.4482117, -112.0709371],[42.922825, -85.6523916]];
        var yellowMarkers = [[40.331837, -79.3783739],[40.0090366, -75.7031451],[40.4750889, -79.833905]];
        var yellowMarkersArray = [];
        var redMarkersArray = [];
        function setContactMarkers(map, locations) {
            var shape = {
                coords: [1, 1, 1, 20, 18, 20, 18 , 1],
                type: 'poly'
            };
            // Create an empty array to hold your red markers
            for (var i = 0; i < redMarkers.length; i++) {
                var place = locations[i];
                var myLatLng = new google.maps.LatLng(place[0], place[1]);
                var marker = new google.maps.Marker({
                    position: myLatLng,
                    map: map,
                    shape: shape
                });
                // Push each red marker to the array
                redMarkersArray.push(marker);
            }
        }
        function setWorkerCompMarkers(map, locations) {
            var shape = {
                coords: [1, 1, 1, 20, 18, 20, 18 , 1],
                type: 'poly'
            };
            // Create an empty array to hold your yellow markers
            for (var i = 0; i < yellowMarkers.length; i++) {
                var place = locations[i];
                var myLatLng = new google.maps.LatLng(place[0], place[1]);
                var marker = new google.maps.Marker({
                    position: myLatLng,
                    map: map,
                    shape: shape,
                    icon: "http://labs.google.com/ridefinder/images/mm_20_yellow.png"
                });
                // Push each yellow marker to the array
                yellowMarkersArray.push(marker);
            }
        }
        function yellowMarkersSwitch(color){
            // map.closeInfoWindow();
            if (document.getElementById(color).checked==false) { // hide the marker
                for (var i=0; i<yellowMarkersArray.length; i++) {
                    yellowMarkersArray[i].setVisible(false);
                }
            }
            else { // show the marker again
                for (var i=0; i<yellowMarkersArray.length; i++) {
                    yellowMarkersArray[i].setVisible(true);
                }
            }
        }
        function redMarkersSwitch(color){
            // map.closeInfoWindow();
            if (document.getElementById(color).checked==false) { // hide the marker
                for (var i=0; i<redMarkersArray.length; i++) {
                    redMarkersArray[i].setVisible(false);
                }
            }
            else { // show the marker again
                for (var i=0; i<yellowMarkersArray.length; i++) {
                    redMarkersArray[i].setVisible(true);
                }
            }
        }
        google.maps.event.addDomListener(window, 'load', initialize);
    </script>
HTML
<body>
    <form name="form1" action=""><strong>Toggles</strong><br />
        <img src="http://labs.google.com/ridefinder/images/mm_20_red.png" width="12" height="20" title="Red Markers" alt="Red Marker" /> 
        <input type="checkbox" name="red" id="red" onclick="redMarkersSwitch('red')" checked="checked" /> Red Markers<br />
        <img src="http://labs.google.com/ridefinder/images/mm_20_yellow.png" width="12" height="20" title="Yellow Markers" alt="Yellow Marker" /> 
        <input type="checkbox" name="yellow" id="yellow" onclick="yellowMarkersSwitch('yellow')" checked="checked" /> Yellow Markers<br />
    </form> <br />
</body>