@Vann Two things that I can think of that might help with this:

1. If possible, running Windows 7 over Windows 10 will make sure that you don't get kicked out of gaming with updates at inopportune times.

2. Dolphin is a very mouse-focused emulator, buuuuut if you run it through Retroarch as a core you can do the emulator settings with a controller instead. Might help with not having to pick up a mouse every time you switch games.