You need to preset them in the property behind the component's value
attribute as you usually do for every UIInput
component. You can do that in the bean's constructor or initialization block.
Here's a basic example:
<h:selectManyCheckbox value="#{bean.selectedItems}">
<f:selectItems value="#{bean.selectItems}" />
</h:selectManyCheckbox>
Bean:
private List<String> selectedItems; // +getter +setter.
private List<SelectItem> selectItems; // +getter.
public Bean() {
// Preset the selected items.
this.selectedItems = new ArrayList<String>();
this.selectedItems.add("valueToBePreselected1");
this.selectedItems.add("valueToBePreselected2");
// Those values should be exactly the same as one of the SelectItem values.
// I.e. the Object#equals() must return true for any of them.
}