be cancelled out, i dont know enough about it, and i would rather have my own tweaks
First, the Addon Manager doesn't "do" any tweaks, it simply read what you ALREADY had in your FSX.CFG file, and display it, allowing to modify it.
Even if you press the Save button, it will simply confirm what was already there. Of course, if you CHANGE a setting, then you press the Save button, it IS "your" setting, exactly as if you modified the FSX.CFG by hand, the only difference is that you used a graphic interface.
The only exception to this, is for settings that are not normally present in the FSX.CFG by default. In THIS case, If you press the Save button, you'll end up adding something, but they are given standard default values anyway.
Of course, this is only relevant to FSX.CFG settings that are global to all sceneries. For Addon Manager specific tweaks, the only that is really significant is the Antipopup value, which has been explained in many other threads here, the others are really minor.