As you point out the wiki and FAQ don't work - I think this is because Google deleted those without asking Simon (he is the guy who made yWriter).
But you can name your chapters anything you want, they don't even have to be numbered.
To rename your chapter from the default name of 'Chapter X', double-left-click the chapter you want to rename, then you will see a box pop up. Where it says 'Title', just write your new chapter name in, then press 'OK'. You can move your chapters around by dragging and dropping them to where you want them to go. You can do the same with scenes - even dragging scenes into different chapters if you want.
yWriter has a lot of features, bit don't get weighed down by how complicated it seems because you might not want all the features anyway. I do recommend to set the 'Autobackup' feature (under Tools>Backup>Set Scene Editor Autobackup Options) to a short interval (I have it set to 5 minutes). If you have these autobackups enabled, it will back up your project on an ongoing basis at that interval. So if, like me, you change something and you wish you hadn't, you go into Tools>Backups>View Autobackups and you will find all your ongoing scene backups sorted by date, then click on the date to find the scene name and saved time. If you make a big change that affects your whole story then I suggest you should back up the whole project under Tools>Backups>Backup Entire Project before you make the change so you will always have your original version before the big change.
Another hint, if you delete scenes, they will not disappear - instead a 'Trash' folder will appear at the bottom of your chapter list and that will have all your deleted scenes in, so you don't lose anything. Simon has made yWriter perfect for people like me who delete a lot, then realise they want the deleted stuff back.
KM