cmptrgeekken's solution works for a single checkbox. I'm assuming you're generating a multiple checkboxes, for a HABTM relation or something similar.
You need to pass a array with the values of the elements that are going to be selected to the method, like this:
$options = array(1 => 'ONE', 'TWO', 'THREE');
$selected = array(1, 3);
echo $form->input('Model.name', array('multiple' => 'checkbox', 'options' => $options, 'selected' => $selected));
is going to generate this:
<div class="input select">
<label for="ModelName">Name</label>
<input name="data[Model][name]" value="" type="hidden">
<div class="checkbox">
<input name="data[Model][name][]" checked="checked" value="1" id="ModelName1" type="checkbox">
<label for="ModelName1" class="selected">ONE</label>
</div>
<div class="checkbox">
<input name="data[Model][name][]" value="2" id="ModelName2" type="checkbox">
<label for="ModelName2">TWO</label>
</div>
<div class="checkbox">
<input name="data[Model][name][]" checked="checked" value="3" id="ModelName3" type="checkbox">
<label for="ModelName3" class="selected">THREE</label>
</div>
</div>
The first and third checkbox checked.
Just remember that you're actually working with a multiple select element that is just displayed as a bunch of checkboxes (Which is IMO better because of the usability).
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