Once you've got everything lined up as it should then after a rotation of the engine, the marks on the pulleys and the timing belt will never line up again, you're quite correct. you need to use the marks on the pressed metal backplate / the 'magic liney-up tool' in the so-called 'locking kit' with the marks on the pulleys (the 'locking kit' actually includes the 'wedges' for locking, but also a couple of means of measuring the marks against the pulleys, checking they're lined up)
So they don't line up again, no, you have to rely on the marks provided by the tool against that marks on the pulleys. if there's a slight deviation (as there could easily be) then of course it's belt off, try again, etc.
Did mine as a 'hand on tutorial' from a mate (who did all the pointing and explaining) and I've had a sleep since then, but the principle's the same. It's not about where the belt is on the pulleys, it's about where the pulleys are in relation to the marks on the engine (ie: where the internals of the engine in relation to other internals of the engine)
or, to put it another way, if you locked the engine, slipped the belt off, threw it in the air, and refitted it in a totally different place, then unlocked the engine, then of course the engine would still run as if nothing had happened, because the timing hasn't altered.