The Superscript style used in MacDraw Pro functions correctly. That is, a superscripted character has its size unchanged while raising the text about one-half line space. This leaves the character size too large if what you want is to create things like footnotes.
Footnotes (as in MacWrite II) use a stylization called Superior. Superior-styled text is raised while the character size is reduced to about 2/3 the original point size. In doing so, the top of the superior-styled text is about even with the top of the surrounding text.
You can simulate Superior stylization by doing the following:
1) Select the character(s) to apply the style
2) Select Superscript in the Style menu
3) Select a character size that's about 2/3 the size of the original. For example, if the surrounding text is 12 point, make the selected character 8 point.