Not sure if this is the right place, however…
It’s possible to ‘save’, say re-ordering in a collection back into a binder by selecting and dragging the list in the collection tab back into the Binder. Drag it to the ‘Binder’ tab, which springs open, and thence to the appropriate folder. The Collection still works fine as it’s effectively just aliases, but the new order’s brought together in a new folder because the originals in the collection have been moved.
It’s reasonably intuitive but not mentioned in the manual so it might be worth adding.
This is mentioned, but in the section on Index Card syncing. This feature was added at the last minute and so I neglected to put anything into the main section on collections. It is a good idea to do so, since it is a core ability and useful for many purposes outside of working with one iPad app.
What this feature basically lets you do is something that has been largely lost in modern outliners: the mark and gather feature. That is, the ability to mark a bunch of items and then gather them together into a single group. Scrivener’s method even takes it a step further by letting you view these marked items in a separate interface so you can better survey them and their relative placements before gathering them.