[SLameN]

Я специально сделал минимум, чтобы удобней читать

<script type="text/javascript">
    function checkAllOne(formName, checkboxName, varChecked) {
        var tablinks = document.getElementById('one').getElementsByTagName('input');
        for (var i = 0, j = tablinks.length; i < j; i++) {
            formName[checkboxName][i].checked = varChecked;
        }
    }

function checkAllTwo(formName, checkboxName, varChecked) {
        var tablinks = document.getElementById('one').getElementsByTagName('input');
        for (var i = 0, j = tablinks.length; i < j; i++) {
            formName[checkboxName][i].checked = varChecked;
        }
    }
</script>

<input type="checkbox" name="total" onClick="checkAllOne(this.form,'phone[]',this.checked)" />Выбрать все
 
<div id='one'>
<input type='checkbox' name='phone[]' />
<input type='checkbox' name='phone[]' />
<input type='checkbox' name='phone[]' />
</div>


<input type="checkbox" name="total" onClick="checkAllTwo(this.form,'phone[]',this.checked)" />Выбрать все
 
<div id='two'>
<input type='checkbox' name='phone[]' />
<input type='checkbox' name='phone[]' />
<input type='checkbox' name='phone[]' />
</div>