If you fill your tank up to the top, that is a full fuel-up. If you can't fill up to the top, that's a partial fuel-up. It doesn't really matter how full your tank is when you add fuel, just make sure you fill it to the top. If you can't fill it all the way up, mark it as a partial.
The whole idea of Fuelly is that it's just a little extra thing you do when you buy fuel normally. You shouldn't need to make extra trips to fuel-up just for Fuelly. Just fill up as you normally would and jot down your usage along the way.