Ok I can help with problem 1, not sure about problem 2. So, for 1. I assume you mean that it looks like Sunshine is on the walls and its lighting your entire map and its not good? Ok. Open the Cell Window, and go to the Lighting Tab. You will see a setting for the Ambient light. Keep that open for reference. Then if you look at the Weather window you have a screen shot of, if you look in the box that says Choose Color, you see 2 drop down menu's and three boxes for RGB channels. This is what chooses the various colors that the weather shines onto your level. So look back on your Cell Lighting window, look at the three numbers under Ambient. Now look at your weather tab, and under the three RGB channels (which in your picture say 122, 171, 180) make sure the two drop down menu's say Ambient then one of the four times of day. (Start with Day I guess) and type in those three numbers. So if your cells ambient lighting is 12, 54, 165, type those three numbers in the respective RGB slot. Then click the Copy button right under those on the weather window. Then change the drop down that currently says Day, to any of the other 3 options. Then click Paste. Change it to another time of day, paste, then the last time of day, and paste. Now the ambient lighting all day will match that of your cell.
Now change the Ambient drop down, to Sunlight (at the bottom) and for all 4 times of day, set the RGB channels to 0, 0, 0. Effectively getting rid of the sunlight.
Now one last step which is for you to customize to your liking. Change the Type drop down to Fog and then make those numbers what you want. Just make sure to make them the same for all 4 times of day, so the fog doesnt mysteriously change all day.
I hope that helps and isnt too confusing. If you have a question on any specific part, let me know.
As for your second issue. I am not sure what you mean. Can you take an ingame screenshot of the issue?
Gunmaster95