For the skies, simply switch the environment under it's menu in the sim. Otherwise, you can set the default env. by going under the track ifo and then browsing for it.
As for logos, they go on cartestures. You'll likely need photoshop or paint shop pro, if you don't, you'll have to use paint, just beware that it can't read .tga's. Once you're in the program, load the default cartexture forthe coaster type you're using. First of all, it's a good idea to familiarize yourself with the cars themselves, you'll have to know where which part goes where. But since most cartextures have the NL logo on them, you can place your logo there and earse the NL logo. Just never overrite the template, especially if you're using paint or something that doesn't support translucentcy, if that alpha channel's removed from teh default testures, you won't be able to select colors anymore.
Theres tutorials on
http://www.digital-experiment.de for them.