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I don't have any help for your first problem of misalignment Steve because I have never come across it, I have only used Art-Wox decks and everything has lined up.

The way I apply them is to prepare the kit deck by gently sanding it completely smooth except for the obvious. That is, remove completely any molded raised lines. I always apply the decking to the kit part before it is installed, starting from one end and moving to the other, then I am able to clamp or 'weight' it overnight uniformly so it does not lift resulting in any bulges as you described. If it bulges it probably means you have raised lines or some kind of 'swarf' underneath it and can be difficult to fix because the adhesive surface relies on its whole area for best contact. The deck adhesive doesn't like to be pulled up and then pressed back down again, it's really only a one shot. You can't glue underneath the bulge because the glue will add bulk unevenly and will result in a visible hump.

The best results are to use only the wood deck's self adhesive and it will stick but you must get the kit deck smooth and clean. I have failed once, made a mess and had to start again with a new deck.

Others will most likely have a different experience and can advise accordingly.