Well the reason I wanted to use the guide is just to learn what to do before playing for real
Easy fix: decide that you're playing for real right now
Quickpawmaud, do the images in section 2.3 of the guide you posted look sort of like what you're looking at in your game right now? An upper level with rooms and a central hallway, and six "down" staircases coming off the hallway. Then a lower level that is supposed to have six "up-down" staircases in the middle, and dug-out rooms on all sides -- but your problem is that those "up-down" stairs don't exist anymore?
If this is close to what you're seeing, then you should be able to fix it the way you proposed (by digging out the outer edges of those lower rooms to get rocks, and using those rocks to construct up-down stairs in those six spots).
But note -- if you've been following the guide more or less, then you've been making stairs this whole time by digging them (by typing d-j for "down" stairs or d-i for "up-down" stairs). If you want to take rocks and turn them into stairs, you'll need to use the building menu instead of the designations menu (b-C-x for constructed "up-down" stairs; note that's a capital C).
On destroying stairs -- can dug stairs be destroyed with d-z ("Remove Up Stairs/Ramps")? It seems that way from the wiki. I can't check in game right now and I've actually never tried to destroy stairs before.