If you want to specify a default shipping method on the checkout form, you just need to set the ‘default attribute' on the ‘shippingMethod' form field as follows:
[MM_Form_Field name='shippingMethod' default="FlatRate-2"]
In order for this to work correctly make sure that you place the SmartTag™ between the MM_Form type='checkout' and /MM_Form SmartTags.
The ‘default' attribute expects a valid shipping method key. To locate the shipping method key go to Checkout Settings > Shipping Methods and then hover over the ‘key' icon next to the shipping method you want to lookup the key for.