Need help understanding why "by pen" (how) comes before "a letter" (what)? Isn't the how placed directly in front of the verb in a sentence?
Korean is rather flexible. As long as you're putting the verb at the end, you're often safe with any combination.
Yet, some are more common/natural than others.
Your options sounds good to me too.
Nicolas is right. Either way works, grammatically speaking, but 볼펜으로 편지를 쓰고 있다 sounds more natural
Now I'm left to wonder how you know my first name (not that I'm very secretive about my identity as evidenced by my profile picture and my username) :)