I ran into a problem recently when wanting to change customers a handling fee of $12 if they did not meet the minimum order limit of $100. The answer was to always have a $12 handling fee, but then give a $12 discount if the order minimum was met.
This is what worked for me:
Shipping Method Settings:
Flat Rate - Enabled
Title - UPS Ground (Will be $0 at time of sale if order minimum has been met)
Type - Per Order
Price - 12
Sort Order - 1
UPS - Enabled
Allowed Methods - Anything but Ground
Free Shipping with Minimum Order Amount - Disabled
Sort Order - 2
Rule Settings:
Rule Information
Rule Name - Minimum Order Limit Met
Description - Order is less than minimum, so a flat rate shipping charge will be applied
Conditions
If ALL of these conditions are TRUE :
Subtotal equals or greater than 100
Actions
Apply - Fixed amount discount for whole cart
Discount Amount - 12
Apply to Shipping Amount - Yes
