1. I've never used IL-2 Stab so I don't know how it works. I assume that it makes changes to your conf.ini. If this is correct, it wouldn't matter if you use Stab or if you edit your conf.ini manually. The other part of the question is that it doesn't matter if you make the change before or after the 4.09b1m patch because the 4.09 beta doesn't touch (overwrite/replace) your conf.ini.
2. The new default skins that can be added with the 4.09b1m are just that--default skins. They are hardcoded into to game so that if no custom skins are selected for a particular aircraft the default skin shows instead. The skins in Enjoyr's patches are custom skins and are used in the campaigns. They can also be used in online dogfights or in QMB or selected by the player in offline missions...but they are not new default skins. You can install all of Enjoyr's skin packs if you wish along with the new default skins pack.
