Piracy

I would use a virtual machine if it's for cracked windows software and especially if it's for someone else (meaning temporally use). You would avoid all the hassle too.

So every wine program runs under prefix (prefix is a whole virtual filesystem that contains the C: drive for the programs to run on). You have to run the crack executable under the same prefix that is used for PaintToolSai. I actually not very familiar about Wine specific, but I think the winetricks tool can help to select prefixes install something and other config.

I'm slightly more familiar with Proton, which it has protontricks tool, but it basically just a winetricks helper for proton. And I don't have a program installed on Wine to test. But for Proton games, I use protontricks --gui then select which game, then select what I want to do with that prefix.

I think if the program is running on the default Wine prefix (I think the default is /home/$USER/.wine) then you can just try running winetricks --gui then select "Select the default wineprefix", next, then run explorer.exe, then execute the crack from the Wine's explorer so it will be executed as if it's a windows program running on windows.