BootstrapCheckboxSetField.ss

<!-- My form field template (for CheckboxSetField) -->
<!-- Changed the li tags to div tags for testing -->
<ul $AttributesHTML>
	<% if $Options.Count %>
		<% loop $Options %>
			<div class="$Class">
				<input id="$ID" class="checkbox-input" name="$Name" type="checkbox" value="$Value"<% if $isChecked %> checked="checked"<% end_if %><% if $isDisabled %> disabled="disabled"<% end_if %> />
				<label for="$ID">$Title</label>
			</div>
		<% end_loop %>
	<% else %>
		<li>No options available</li>
	<% end_if %>
</ul>

CheckboxSetField.ss

<!-- Original form field template (for CheckboxSetField) -->
<ul $AttributesHTML>
	<% if $Options.Count %>
		<% loop $Options %>
			<li class="$Class">
				<input id="$ID" class="checkbox" name="$Name" type="checkbox" value="$Value"<% if $isChecked %> checked="checked"<% end_if %><% if $isDisabled %> disabled="disabled"<% end_if %> />
				<label for="$ID">$Title</label>
			</li> 
		<% end_loop %>
	<% else %>
		<li>No options available</li>
	<% end_if %>
</ul>

Page.php

class Page_Controller extends ContentController {
public function NewsletterForm() {
      $checkboxArray = $this->RetrieveMailingLists();
      $form = Form::create(
          $this,
          __FUNCTION__,
          FieldList::create(
							HeaderField::create('HeaderTitle','Select which mail listings you would like sent to this email',4),
							EmailField::create('Email','Email(Required)')
							->setAttribute('placeholder','e.g. JohnDoe@provider.com')
							->addExtraClass('form-control'),
              TextField::create('FirstName','First Name (Optional)')
							->setAttribute('placeholder','e.g. John')
							->addExtraClass('form-control'),
              TextField::create('Surname','Last Name (Optional)')
							->setAttribute('placeholder','e.g. Doe')
							->addExtraClass('form-control'),
              CheckboxSetField::create(
              'MailingListsSelection',
              'I would like to recieve the following mailing lists',
              $checkboxArray)
              ->addExtraClass('checkbox')
							->setTemplate('BootstrapCheckboxSetField')
          ),
          FieldList::create(
            FormAction::create('handleNewsletterSubscription','Subscribe')
                ->setUseButtonTag(true)
                ->addExtraClass('btn btn-success')
          ),
          RequiredFields::create('Email','MailingLists')
      );

      $form->addExtraClass('form-style')
      ->setAttribute('name','NewsletterForm')
			->customise(array(
				'ErrorResponse' => $this->ErrorResponse(),
				'SuccessResponse' => $this->SuccessResponse()
			));
      return $form;
  }
  }