I was just quick saving a lot, and didnt bother to really use the "save function" so i had to start from the beggining after hours and hours, what happened?

Quick-saving in SS2 is a bit iffy to say the least.  What might've happened is that you or someone else started a new game.  This prompts SS2 to automacially overwrite the last quick save.  Anytime you enter a new area (via bulkhead or anytime after a loading screen) the game will auto-save.  In other words, it's best to always have an actual save whenever you're done playing.

Quicksave overwriting is actually fixed by the SS2Tool, forcing the quicksave feature to make a regular save in the last save slot. And even if he wasn't using that, his quicksave would not have been older than the last time he saved, but younger.
Did you try using the quickload key to load your save game?

loading a previous save overwrites autosave and quicksave, unless you are using a ss2tool fixed install of ss2 (in that case, only the autosave gets overwritten). it's just the way the game works.

one way or another, making a normal save every 30 minutes is a good idea, especially when playing ss2.

No, I mean the last normal saveslot.