I am not entirely sure what you are looking for.
If you want to automatically transform words written in the original Arabic (such as كان) into its grammatically correct transliteration (in this case kāna), then it is obvious that no such automatic transformation is possible. It is a peculiar feature of the Arabic language that it only writes the consonants and long vowels and leaves out the short vowels. it is, however, the short vowels which determine the exact meaning of a word and its function in a sentence. Thus, as I am sure you know, most words in Arabic can be interpreted differently: for example كتب can mean both kataba (verb) and kutub (noun), depending on its use in the sentence.
So, if this is what you are looking for, then there is no way to transform Arabic into transliteration. You could, however, use
arabluatex which allows you to write an Arabic text in an idiosyncratic transliteration format which then can be displayed either in Arabic letters or on a transliterated format.
If you merely want to input special characters such as ā, š, ṣ, ʾ, ʿ, ḫ, ġ and so on, then this is very easy (provided you either use the modern formats LuaLaTeX or XeLaTeX, or set your system up for unicode; all this is explained here).
On a Mac, you can download a diacritic keyboard layout (e.g. from here) and set it up. In order to type ḫ, for example, you would have to press ALT+f.
On a PC you can use a tool such as Clavier to design your own shortcuts.