First, I come up with a mission name. For example, for my Mun missions, I named I named it Munar. Then I use roman numerals for each general design. Then, if I need to make a small change, I add a letter to the end. So, for example, I might make the Munar I for trying to just get into orbit around the Mun. Then I might realize that it works so well I just need to add legs to the top stage. So, I add legs and call it the Munar IA. Then, I may try to bring a bigger lander to the Mun, so I build one and call it the Munar II. Then I make a smallish change and call it the Munar IIA. If something is experimental then I add "X/" before the roman numerals.