Yeah, you can work in ends as you go, but I don't usually and here's why. On a project that is not super easy-peasy I always like to make room for having to take it apart. I have knit something that I think is perfect and later realize, oops, big mistake back there. If I have worked in my ends it makes it a lot harder to undo. Also if I am seaming I sometimes hide a few of the ends in the seams and I have to get to that point before I'm ready for them. I guess I just put up with them. If they are extremely long I shorten those I don't need to about 5 or 6 inches. I've been using the duplicate stitch method of hiding in ends quite a bit and it needs a bit more to work with.
I think some folks coil troublesome ends up and maybe fasten them to an edge or something, don't know for sure.
I vote no on knots.