When writing, or indeed speaking, do not begin sentences with any of these phrases.
“Let’s be clear” admits that, up to this point, you have been obscure.
“To be honest” implies that you’ve been lying until now.
“Putting it simply” suggests you’ve been making it sound more complicated than it is.
Your writing and your speech should always be as clear, honest and simple as you can make it. Clarity, honesty and simplicity are not optional extras that you can use occasionally to decorate your communication.