When do you stop reading books cover to cover?
You stop reading books cover to cover when you don't need all the information between the covers of the books.

If you take a textbook on topology and flip to the middle, it will probably be largely uninterpretable because you don't know the terminology, previously proved theorems, and so on.  You can still glance through the chapter on the material that you really need to know to get an idea of what you're completely missing.  If you can select a subset of earlier chapters that let you understand the later one, great!  If not, read the whole thing.  If that's still not enough, get another textbook or talk to someone who knows the subject well.

You'll have to make the call regarding when it's better to proceed in this way and when it's more efficient to simply start at the beginning and go through it all.  If you need to know something well, this is often the approach to take not because the other wouldn't work as well in principle, but because in practice the temptation to be less thorough than one really needs to be is often too great.