If you're viewing this on a mobile device, you may find that the text entry buttons are easier to work with in landscape orientation.
The main page contains much more information about the ruleset that the program follows.
Generally speaking, use of the "secondary" and Persian-specific letters is optional. They are provided for convenience, but Persian pe (پ), for example, will be treated the same as Arabic bā’ (ب); tā’ marbūṭah (ة) is considered equivalent to hā’ (ه); and so forth. Please refer to the Wikipedia entry on abjad numerals, which lists (most of) the letter values. I've also posted a table highlighting the differences between the Mashriqi and Maghribi systems.
You may notice that two of the buttons above are practically indistinguishable. One of them is for Arabic alif maqṣūrah (ى), and the other is for Persian ye (ی). Trust me, they're different letters! Both will receive the same abjad value as Arabic yā’ (ي), in any case.