On the Math tab sheet of the User SetupUser_setup.tex dialog box, you can set options for numbered equations, the size and placement of mathematical objects (fractionsFractions.tex, radicalsRadicals.tex and math namesMath_names.tex), and the Math/TextMath_text.tex toggle.
The program also has built-in defaults that govern the appearance of mathematics. You can turn off these defaults and specify the mathematics appearance settingsChanging_math_specs.tex you want from the Tag Appearance dialog box.