You can overide the path of your multimedia binary using template code as long as you have structure group created for same path.
Ex if you want to publish particular binary to \css\images folder, you first have to create the structure group for same path(\css\images) and use the structure group id in the following code to publish the binary.
engine.AddBinary(Binary.Id, templateID, binaryStructureGroupID, Binary.BinaryContent.GetByteArray(), Binary.FileName);