If you're starting pretty fresh with the science material, you need two things more than anything else: organization and a solid foundation. One major reason why a lot of people don't find Khan videos, textbooks, or non-MCAT websites (like general study sites) helpful is that they're great at providing the material, but they don't (and don't aim to) set it up in a coherent order. You can watch all the Khan videos you want, but if you don't know which topics they tie into, you won't retain much. It'll all just seem like snippets of info.
If you already have a Kaplan set, though, you can use it to make a plan. I'd recommend going through their chapters
in order and
very slowly. Think of their books as a framework in which you can fit plenty of other materials. For example, when you read about fluids, stop every couple of pages and ask yourself questions - does this relate to anything you already know, does it tie into other chapters, etc. At the same time, you can watch all of the Khan videos and whatever else you can find, which will now make more sense. Don't watch a video unless you've already read about the same topic, and try not to move on unless you understand what's being said. You can also use the Kaplan books as a gauge - if you stumble across anything on the internet that's not covered by Kaplan, there's a solid chance (but not a guarantee) that it's not necessary for the MCAT. This is why you don't want to use straight-up textbooks - you'll cover a TON of material that isn't high-yield on the exam.
The second key to content "re-learning" is to start easy and work your way to harder concepts. This is why I wouldn't necessarily recommend starting with prep books that are famous for being difficult - they're great, but they're also dense and complex. That can come later in your prep. If you start out fully understanding things like stoichiometry, projectile motion, the cell, etc., it'll make your prep 100x more efficient when you reach topics like electrochem, optics, and glycolysis.
Good luck