wa when used as an article.But personally, I don't follow a specific set of transliteration system.
I prefer the system where each kana is assigned to one unique romaji. I.e. I will retain "wo". But there are exceptions.
I use "wa" instead of "ha". And also for certain words like Tokyo, I use the more commonly recognized "Tokyo" instead of "Toukyou".
I just use whichever easier to read and decipher.
Ya. Forgot to elaborate on that.wa when used as an article.
ha when used within a word for me.
Night GumiGtbgn