In either case, the safest choice is choosing boots that are tall enough to be covered by the hemline of the skirt. This will keep the lines of your outfit long and lean.
For casual long skirts, let the fullness of the skirt be your guide.
Slouchy, heeled, flat, and even chunky tall boots will work with a fuller skirt like the one shown here, while long narrow skirts work best with heeled and close-fitting boot styles.
Pictured: Patchwork Print Skirt from Newport-News.com.