Silandor: The manual save overwrites the manual slot based on your control.
Unfortunately this is false, and I even guess it's a bug, your manual save, I mean everything you save with the in-game devices, will ALSO be overwritten as soon as you leave your ship, making it basically useless. if this flaw was not there and the manual save would be kept 'as is' , then all would be fine and would corrispond to what the update 4.0 notes are saying, but alas this ain't so, your manual save gets constantly overwritten because you are quite always using your ship.
Also useless because of this is the renaming feature (what sense does it make to rename a save if it changes all the time?)
The system as it works now (4.05) simply has 2 save slots, the 60 seconds autosave will be in slot 1, slot 2 will contain the in-game device saves until you jump out of your ship in which case slot 1 is overwritten, what was in slot 1 before will be moved in slot 2 and what was in slot 2 before will simply vanish. For me, the in-game saving devices (beacons, save point, POI flag) suddenly become all useless - or I need not going in my ship, that's ridiculous.
In essence, you have 1 save and 1 other backup that is also very recent. IMO It's a pain compared to how it was before but convenient to base-builders and grinders who don't jump out of their ship all the time, not causing the 2nd slot to be overwritten, but else there are a lot of playing scenarios which make the new system not useful.
I expect a lot of players making feedbacks or bug reports to Hello Games which then get aware of the problem and hopefully eradicate this behavior in the next patches.