how can i set charge for shipping per sales order

Use the shipping cost field under the shipping subtab of the sales order

I was not clear I want that if certain parameters are met charge shipping , i want to do this on the slaes order level and not on the shipping method

Oh I see. Depending on how complex your parameters you might be able to do using a workflow. Otherwise it would be a script You can setup free shipping items so if you select those as the shipping method it would be no shipping charges (like setup a shipping item of UPS ground - free and UPS Ground). You can also add shipping rules that adjusts rates like Quantity or Weight based rules. Not sure if that would cover it