Or do you just keep them as they are under that very project of Sonar and hope to find the same patch with looking back on that earlier project?
'Song persistence' has its place. I usually reserve that for some song-specific minor tweaks of whatever preset I'm using. I'm sure that I'm in the minority here, but I rarely start from a factory preset.
Do you save them under other names ( e g save as: "fav bass no 1") or something?
Almost without exception. If I do intend to modify a preset, I perform a 'Save As' operation
first. It will go into another subfolder tree of custom presets. I try to preserve the originals and keep my creations separated.
I hope that "save as" in Z3TA doesn't rename the factory name, or does it??
No. Not Save
As.