Certain shipping methods are either incompatible with your business, painfully slow, or too expensive to use. By default SKULabs only disables Library Mail and Media Mail. You can configure your "Enabled Methods" by clicking settings then shipping then enabled methods.
Enabled shipping methods are used in the "Least expensive calculation" default shipping options. To exclude certain shipping methods from this calculation, you can disable them from Settings page > Shipping tab > Enabled methods.
Simply check the box under the Active column next to a method you want to exclude and click save.