I'm trying to achieve the following: customers can choose in the checkout (either at shipping method or payment information) between two options. First option is one in which 4% of fee is added as we simply collect the order for them from the different suppliers. In the second option we not only collect, but we also make sure that the order is being optimized with regard to transportation (as different suppliers will send in boxes which are half full). In this case we charge 10%, as the customer (picking it up themselves) has less boxes to transport.
The solution I came up with/found is to set up a negative discount in "shopping cart price rules" (not optimal as core modification is required) for both options. Then link these to two flate rate shipping options. However, I'm using the Matrix Rates module in order to calculate the shippings costs dependend on the weight. As a result I can only link one option, which is clearly not what I'm looking for.
Hope my explanation is clear enough. Is there anyone who might ran into something alike, or can give me some direction/ideas what other options are available?
Thanks to you all for your responses, we have decided (as advised by one of you as well) to simplify the process itself. As we think we run into too much inflexible modifications.