To change the default shipping method selected at checkout, from the store dashboard go to:
> Store Settings > Checkout > Shipping

From within this page, the top dropdown menu labelled 'Default to select at basket' gives you the option to alter the default shipping. The default shipping method chosen will then always be pre-selected at basket (can be changed by your customers).
The tick-box directly underneath labelled 'Shipping is per item' is an additional setting which either applies the shipping cost to the entire basked or to individual products.
*Beside each of these settings is a description which informs you of what they each entail - please read them carefully*
(*Don't forget to click 'Save Changes' after making alterations*)