I don't think my boots are specific Whites/Aqualung boots.
My suit came without boots, I tried a number on until I got the best 'fit'.
I always put the boots on after the suit. The only piece of advice is not to walk around in the socks until after you have put the boots on. This isn't unique to the Whites suit, its the same for any suit with rock boots.
You often hear of people who have 'leaky' suits. Often the holes are in the soles of the feet, or the leg or back of the suit. From where people stand on the suit when changing. Best advice I was given is get a changing mat, and avoid standing on the suit.
Gareth
The Whites/Aqualung Fusion boots were designed to be paired with the Fusion drysuit. They have a wide velcro strip along the inside-back of the boots to mate up with the velcro strip on the sock of the drysuit. There is also velcro around the cuff of the boot with additional tabs in front, back , and on each side, that connects to the loop velvro near the cuff of the skin.
While I don't have much experience with drysuits, I like having the boots attached to avoid the possibility of creating the damage you referenced in your post. The design allows me to just slide my foot into the boot directly with no fuss when donning the suit and nothing further to tend to except a velcro strap that goes around the ankle of the boot to limit the ingress of air into that part of the suit.
YMMV I guess, but so far they are working well for me.
-Z