You don't need a fancy GUI program for this, despite some guides like TMW's using them.
All you need is UMU-Launcher, which is a launcher for Valve's Proton. You could use stock Wine to run visual novels just fine (with some tweaks, like copying over Windows fonts to the wineprefix and executing the VN with the env LANG set to ja_JP.UTF-8, essentially as if you were using Locale Emulator on Windows), but some stuff like videos are hit or miss, and that's because Wine relies on the system's GStreamer, which can be messy.
Sticking to Proton (specifically Proton-GE) will ensure that most VNs play videos, since it uses a bundled GStreamer version that just works.