I don't think there's a problem if it sticks out. People just think it looks better if it's flush with the tank. You don't have to fill the tank to the max.. just enough to cover the hole in the carto (but as long as you're filling the tank, might as well fill it more than just over the hole).
The filler in the carto shouldn't fill all the way to the top with juice.. doesn't need to, as long as the juice is wicking in through the hole it'll be fine. If you are chain vaping and get a dry hit.. just give a dry pull (suck on the carto without firing the device) to pull some juice up into the carto. There are several chibi threads on here, read through them and watch the videos on how to assemble and fill them.
I love my chibi tank! It got the $8 one with the included punched carto. Now I punch my own cartos. It's the best vaping product I've ever bought!