We are beginning a new home and are considering flooring options. Is there any reason that treazzo floors aren't being used much? Are they easy to care for?

I am laying ceramic tile over concrete slab in my family room basement. The carpet that I ripped out had so many pet stains from previous owners that I cleaned the concrete with a mixture of clorox and then put kilz over the concrete to seal it. Will that affect the bonding of the tile to the concrete?? If so, how do I compensate? Also, there a minor low and high spots in the floor and the tiles I chose are 13.4" square so there are some places that they "rock" a bit. I spoke with a clerk at Lowe's who said she'd just built the adhesive up a bit, let it set up for a few minutes and then use it to level the tile?? Is that the proper manner of correcting this problem??? I appreciate any help. I'm tiling the floor this weekend and want to get it right. Any tips from anybody for keeping the tiles straight other than chalk lines? Thanks for any help you can give.