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  icon next to the shipping method you want to lookup the key for.