What do you mean by filter pad? Do you mean a cartridge or a piece of sponge pad?
On the face of it no, putting filter media the wrong way round shouldnt affect your cycle. Depends what the filter media is though. Obviously a filter is designed to work in a particular order so it better to have it set up correctly, but many people have filters set up differently to others without too much issue.
Could you give some more details on what you are doing to cycle the tank? How long have you been going? What stage are you stuck at? Perhaps we can see something wrong with what you are doing, or reassure you that everything is good and just needs more time.