If i have my saves (which i have) that i kept from the time i had this game in CD support, would they work in this version?

Yeah, but if you don't changed your PC name.
My old saves from CD-version (patched to 1.0.5b) are working fine.

"DarkStone writes the computer name directly into the save file. If you go to another machine
and it does not have exactly the same name, it will not recognize your characters."

You still can hexedit "characters.lpl". Write your new PC name in header and save should work.
Also, you can just rename you PC to that computer name that you used before.