Settings dialog box can be accessed by selecting Settings | Settings... menu command.

Language: Specifies Indian language
Indic font: Specifies default font for selected Indian language
English: Specifies default font of English text
Keyboard: Specifies the keyboard used for Indian languages. [Phonetic, Brhkbd, Inscript]
Pan-Indic keyboard: Use Pan-Indic keyboard which is common across all Indian scripts. If this option is unchecked then the legacy phonetic keyboards are used
Output: Select output type. [Indic, ISO15919, IAST]
Indian numerals: Use Indian numerals instead of English numerals
Auto completion: Enable/Disable auto completion. Read auto completion topic
Tamil consonant numerals: Subscript numerals (ex: க₂, க₃, க₄) are used for க, ச, ஜ, ட, த, ப consonants if this option is selected
Screen color: Specifies the screen color