In order to edit your saves for use with save editors like PKHeX or Sky Editor, you must first be able to backup/restore your save file from a cartridge. There are many ways this can be accomplished, and it all depends on what hardware you have available. The following methods are listed in order of recommendation. Pick the first one you have the hardware to use.
When this guide refers to IR games, it refers to games with an IR port like Pokemon HeartGold, SoulSilver, Black, White, Black 2