Thunderbird has the somewhat strange default behaviour of starting replies below the quoted message. Fortunately there is an option to change this, and I’m mentioning it here as it’s a little hidden away and I had trouble finding it myself.
Click Tools (from the menu bar), then Account Settings. Now choose Composition and Addressing which appears under your account name on the left. Underneath Automatically quote the original message when replying (which should be checked) you can then change start my reply below the quote to start my reply above the quote. Easy as that!