So it seems that the only way to change the above things would be through the WindowsBlind section, Modify Style - Colours - Change System Colours, but doing it that way, it don't look like I can change it through the SkinStudio later. Is that right or am I missing something ?
I believe changing the system colors via WindowBlinds is changing the same thing that you change within SkinStudio system colors. I haven't double-checked to be sure right now. In other words, you should be able to change a system color via WB, close WB, open the skin in SkinStudio, and see the changed system color there. Then you should be able to change it again (and save changes), close the skin, look at the system colors again in WB, and see the new color you just entered in SkinStudio.