Silent Hunter 3 has always run reasonably well under all versions of Wine. The starting point for information is wineHQ
https://appdb.winehq.org/appview.php?iAppId=3793
Wine is not the most friendly thing in the world to set up. Hence Proton I guess. I heartily recommend you look at a howto guide, e.g.
https://www.wikihow.com/Use-Wine-on-Linux
If you got the game from Steam then search the Steam SH3 community
https://steamcommunity.com/app/15210/discussions/ , there used to be some step by step instructions for Linux/Wine there.
In brief:
Wine uses an area of the user's home directory for each wine installation. This is referred to by a system variable called a WINEPREFIX. The default location is the hidden directory .wine. There's a subdirectory drive_c in there which is all your windows files in the usual windows directory structure.
To set it all up type the following from the terminal:
winecfg
This also allows you to tailor the system behaviour for each installed application.
I don't know what proton does with its files, to use an existing Proton installation you might have to do something like
WINEPREFIX=~/.proton winecfg
You have to install your applications just like windows, so use commands like
wine 'install.exe'
There's a utility called winetricks which lets you add more dlls in your virtual C drive to get stuff to work. For example the Vulkan implementation of directx would be installed with
winetricks dxvk
Which might get you back to your white smoke bug! BEWARE - it's hard to go back!
To get widescreen working in SH3 you need to run winecfg, select the libraries tab and override d3d9, msvcp71 and msvcr71. This makes wine try to use local versions of these dll's in the SH3 directory which have been messed with to get widescreen working.
It's not so hard once you get used to it.... Honest...