Dunno what you've done to set it up like that... looks to me like you've downloaded a modded Tukui and/or it's conflicted with other addons you have installed. That banner across the bottom, for example, woul drive me crazy! You've got two unit frames set up as well, one above your quickbar (Tukui default) and one in the top-left (base UI default but reskinned - possibly X-PERL?).
The two boxes you're referring to I'm guessing are the grey boxes along the bottom centre? If you look at my & Newts' UIs, you can see that we've got dual 6-button quickbars in those boxes - not sure how Newts has set his up, but mine is actually one bar in each box, 12 buttons to a bar and ordered in two rows (1 - 6 on the top, 7 - 12 on the bottom). There's also a large grey box in between these two boxes, but I'm not sure where yours has gone. This larger box fits two standard 12-button rows one on top of the other. The mod you need is Bartender - you can set up as many as 12 different quickbars and custimise each one, be it a teeny tiny 4-button shapeshifting bar, the aforementioned 6x2 quickbar block for the sides or my own 3x4 block for crafting & mounts as seen between my quickbar hub and loot window/bag frame. It'll also let you shift that bar you have on your screen now so that it fits better between the two grey blocks - I find that on default Tukui settings, a Bartender scale of 0.85 with button padding 1 fits quite snugly. You can ditch the numbers displayed on the buttons too, and do away with that annoying menu bar (buttons for character pane, dungeon finder, achievements, quests etc that can all be accessed by shortcuts or by middle-clicking your minimap) and bag frame (Tukui has a hidden bag frame that you can toggoe on and off in the bag window).
If you don't want the grey boxes on either side, hover your mouse over the outer edges - left edge for the left box, right edge for the right box. You should get a button popup that'll allow you to collapse the frame completely, leaving that area clear for other things. I can only hope that this is why you don't have a central box. If so, sweeping your mouse over the area slowly will bring up a maximising button that should return the box in all its glory. If not, I can't help you.