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Patience is a virue, you know.

Anyway, I am not sure how easy this will be to explain, without a practical demonstration. When I want to have the vanishing points at a substantial distance -- as when one of the three is actually inside the page, for instance -- what I do is this: cheat.

Basically, it's a combination of the machine and eyeballing. I unlock the hub, so the arm turns freely, then I lock it again with the small thumb lock. This allows for quick lock and turn moves. With the arm locked, I draw three parallel lines, maybe half an inch apart. Less, if it's a small drawing, like a single panel on a page. That done, I unlock the arm, rotate it ever so slightly, lock it again, slide it down half an inch, and draw three more parallel lines. Repeat this process until the bottom of the page or panel is reached. By then, you will find the arm is considerably out of true with your original three lines.

Takes a bit of practice, estimating just where you want to place the hub, and how close together you want the parallel lines. (And discovering if this time you might need four, or two, instead of three.) The end result, if you do it right, is an optical illusion. It looks like there is perspective, but there really isn't.

As to your second question -- if I am understanding you correctly, the only downside of the machine is that there is no way to get the lines to come to an accurate single point. The center on which the arms rotate is somewhere inside the hub, so the pencil cannot get anywhere near it. Plus, the arm does not generate a true perspective, more of a forced one.

So for vanishing points actually inside the image (an extreme down shot, for instance) I fall back on the ol' set-square. ("Triangle", to civilians.) Having a couple of those, with different length sides, can be very handy.