HWaus
Did you take notes while going through each chapter, and did you ever refer back to those notes?
You should definitely take notes, or even better, flashcards. And yes, refer back to them, especially when it's close to test day and you're mostly trying to review what you've already learned.
A good thing to do is, whenever the chapter tells you some rule or process, put pencil to paper and work out a couple of examples on your own. For instance, if you're reading the Sentence Correction guide, try to come up with some example sentences that use the rule you've just learned.
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Should OG questions be attempted during or after the completion of the book set?
This is probably kind of an annoying answer, but my answer is 'both' and also 'it depends'. It depends mostly on your timeline (are you taking the test soon, or do you have a while?) and the level you're currently at (do you just need a quick refresher on the content, or are you learning it from scratch?) There's not much point in doing OG problems that are way above your level, regardless of where your level is. And if you're an absolute beginner, most OG problems may be above your level right now. In that case, it's better to focus on learning the material methodically before you do official problems.
But if you're working on a topic and it's mostly familiar to you, and you're starting to feel pretty comfortable with it, you can also do sets of problems on that topic from the Official Guide.
And if your test is coming up soon... you should definitely be doing mixed, timed sets of random problems from the OG, no matter what.
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Has anyone gone through the set twice over the course of their preparation?
Sure! Review is important.
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Should
MGMAT Books be used concurrently whilst taking a GMAT course such as TTP or egmat?
I'm biased, but I'd recommend the MPrep course along with the books, or GMAT Interact. That way your homework will actually come from those specific books and you'll be able to get guidance from folks who are very familiar with them.