How is a new FID generated ?
Is it done by the player or by emplode ?
As far as I can see it's "simply" going up,
so were is the last used valued stored ?

It's done by Emplode (or Emptool, or JEmpeg), which "simply" use the lowest number that's not already in use.

To put it in other words:
If I add a song "manually" where do I find the FID for it and
how do I make sure it isn't overwritten by the next upload ?!

You can use any unused fid, and subsequent uploads will automatically avoid it.

And can I force the player to recreate it's Database ?
I don't want to delete it and have a full rebuild,
just an incremental build...

You have to do a full rebuild; there's no code for incremental building.

Peter