i meant you can drag and drop your file into the reply field if you want somebody to have a look. if your circles are on the surface through the panelling tools it should actually intersect. the sequence is usually easy and i assume you did some splitting already? or does it not work in your case? splitting works as followed: either you select the surface first and then enter the command it will only ask you to select the splitting objects (the objects which will be used as knifes) in your case the circles. or you enter the command first it will ask you for objects to split, after selecting them you hit space or enter and then it asks you for the splitting objects. you complete the command by hitting enter or space which is clear by now i hope otherwise i would be wondering how you get around with paneling tools
either way after the command has finished you simply selects the cut out parts and delete them to make the holes visible. splitting does not trim the parts out it just cuts them, the removing still has to be done in case that was the misunderstanding, otherwise post your file here.