An increase only in a type of transport

I would like to apply an increase of a certain fixed amount to the orders made ​​by a particular carrier.

The amount is not the trasport cost but costs of packaging to add only if the user chooses that particular carrier.

How can I do?

If you use manual shipping methods, you can just increase the prices in your methods.
if you use UPS, Fedex or Australia Post, there is a handling fees option that you can set in the shipping method options for that.