I haven't read all of these comments yet... I have a couple different ways that I scrap.
For CT, I already know the kit I will use, so I choose photos/story to match, then a template based on the photos and story I chose. I stick primarily with that kit, and I pile things on my page, usually going from bottom layer to top based on the layers of the template.
For non CT scrapping, I typically start with photos/story in mind, choose a template, then search my stash for the main kit or collection I will use. I am more likely to branch out to other kits by the same designer, or other parts of the BYOC or collection I'm using. I would love to say I have an awesome organization to be able to find things like this quickly, but I really just rely on the TLP shop a lot of the time. I glance through the past BYOC or MPM or M3 or story teller collections and can can typically remember buying parts of whichever when it was on sale, so I know which papers/elements I have just by looking in the shop, and I know where they are in my stash because I keep things stored by designer.
In short... knowing how you scrap, or choose to scrap, will help you gain your own efficiencies. I know "practice makes perfect" was essentially noted above, and it's true. When you have your own process down, you're faster at it than others.
If you like to mix and match things, maybe storing things by kit isn't helpful for you... perhaps you break apart your kits and store them by type instead (providing the filenames are enough info for you when marking down credits) - maybe keeping things by designer, but not in specific kit folders... idk, just a thought!