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It's a pity to give up, I would have helped more if you'd provided the information that was asked for.
@timbuck2 Right-click on XEX file and choose "open with other application", then look for and select the program you want to associate with this type of file. Wine programs might not show and you will need to click on "use a custom command" and browse to the windows exe file. To run with wine you must prefix what you find with wine, eg wine " /home/USER/.wine/drive_c/Program Files/Someprogram/someprogram.exe" and also don't forget to enclose the path in "" because of any spaces in folder/file names.Then tick the box for "Use as default for this kind of file". Close the dialogs.Repeat for a HYP file and that should associate those files with the different programs.
A little. Just a tip when asking for support, please provide as much information as possible. For example, a quick Google of WinGuide.exe lead me to https://osdn.net/projects/sfnet_theguide/ is that right? So we'll need the actual links and names of the primary software. Most of us won't know what these are or where they come from or what they do.
You'll need to tell us what programs they are each for. Cheers.