I'm actually not using any special program but just the language setting of Windows. It's called "Languages and keyboard settings" (or something similar to that). When you add Japanese you should be able to change between latin letters and a keyboard with Japanese characters. With that you can just type your Japanese words as you would with your English keyboard and it should transfer into Hiragana. You then also get a list of options to choose from like all the variations in Hiragana, Katakana and Kanji of the same arrangement of syllables, e.g. hana はな ハナ 花
For me that's just the easiest way (and I guess also a common one) to do it because it gives you suggestions on what words you probably wanted to write (like when I typed hana, it already suggested "hanashimasu").