It is up to you whether you charge Fliiiight during use, or charge it between uses.
When plugged in, Fliiiight is able to slightly increase the strength of virtual inertia to optimize road feel. When unplugged, it slightly decreases the strength of virtual inertia to extend your wireless riding time.
Modern lithium ion batteries have controls to protect them from being overcharged. Leaving the trainer plugged in is therefore safe, however the lifespan of the batteries can be maximized if Fliiiight is not left on the charger constantly when the battery is already charged.