There are a couple of things you can consider, some of it, oddly, is in the manual.
for instance, in chapter 7 of the manual which you can find here, there is a button which is clearly marked "open c: drive".
So that should get you closer to the files.
What isn't in the manual, is that you should consider using a symbolic link. Lets make a few assumptions for this example.
1- Lets assume that you would like your mods in /home/elder/mods
2- Lets assume that your game mods are in /home/elder/.cxoffice/bottle_name/drive_c/Program Files/a_game/mods (notice the dot before cxoffice)
1- Move your files over to /home/elder/mods
2- Remove the old game mode directory
After, what you would do in a terminal is:
ln -s /home/elder/.cxoffice/bottle_name/drive_c/Program\ Files/a_game/mods /home/elder/mods
A couple of things about the line above:
1- Notice the \ character right after "Program" it's an escape character to use the space right after it. Unix system, like Linux, doesn't allow such stupidity, so you have to use \ to use a space in a file or folder name. Pressing TAB after having typed the first few letters of "Program" should auto-complete the name properly without you having to remember this.
2- There is a space between the two paths, right after the first "mods". In other words, your write [origin path] space [destination path]
3- After this, anything put in the mod folder for your game will actually appear in your /home/mods folder.
4- You could also do this with sub-directories within the mods folder so as to separate your game files per game.
5- Typing "man ln" in the terminal will give the manual in terminal to finish off your education on the matter of symbolic links.
So yeah, RTFM has a foundation of truth, but I do believe in a more thorough explanation as well.