The "save" function on the game is painfully simple. It saves to exactly the same file name as the one you opened. Be aware - not the same file, the same file name.
So, if you open Spring 01, and play thru the Summer and Fall auto-saves, and then Esc-Save, it will save to... Spring 01. (And overwrite that save.)
The only way to save Spring 01 is to have made a copy w/ a diff name - actually, "Copy of Spring 01" is perfectly adequate.
Also, if the game is running and you rename that file (in this case, Spring 01), all hell breaks loose when you then save. Not right then, but months or seasons down the road - Nemesis Error, restart game. (See stickied thread at top of Bugs subforum.)
My PC is slow, so I often have to save between autosaves. When I do, I rename those with something significant - and I always do this when a game is NOT RUNNING. DF can be open to the first menu, but no open game up and running - ever.
1) First, I rename the "Region 1" folder with something more significant - eventually with the name of the fortress, but at first maybe the world name.
2) I make a copy of this, and label it "clean" - I never start a game from my clean copy, but make a copy of that, rename it, then work from that.
3) I add a date to my saves, after I save them and while no active game is up and running. 01.01.01 is day 1, 01.02.03 is the 3rd day of the 2nd month of the 1st year, etc. So I can actually tell which is which.
4) When done, I rename the save with the new quitting date info. Repeat.
So, I can look and see "GameName Aut 201", but I also might see my own save 01.07.15 - from middle of the first month of Autumn. I open that, play, maybe thru an autosave, then note the date and Esc-save - and then redate that save. When I restart, that's the one I know to open.