I would experiment first
Lay then down on some saw horses to see which ones mate together best, having the bottoms as a reference. Flip them around to see which grains look best from the top. I don't know how you will glue them together IF you don't have straight and square edges. Do you plan to the straighten all the edges? You can leave the outside edges "live", but the interior mating edges should be straightened. On the saw horses, you can easily reach underneath to put a shim so they will level out best. You can't do that on a solid surface table.
I would let them "self adjust" when gluing them up rather than trying to use dowels, BUT plan on flattening BOTH sides. Adjust them under the router to remove a minimum amount of material and still get them as flat as possible.
See what you get when done as suggested above. A photo would help after that.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)
Last edited by woodnthings; 10-02-2018 at 02:50 PM.