The best way and easyest is to leave it the eay it is you will never get it perfect anyhow. YOu cant put concrete ontop of concrete it will not bond. I would make sure it is square and the snap 2 chaulk lines 1 north south 1 east west. Then start in the middle and work your way to one wall then back your way all the way around the room in a circle till you are at the door way so you can get out. Just fill low spots that you can see if corners dont line up with your thinset. You can lay the thinset pretty thick in places you need to if you know what I mean. Any questions mail me. Good luck.