Guild Wars 2

Right now I only have the Ascended version of the Prototype Fractal Capacitor. If I were to use the charr back pack cosmetic on it, will i still be able to use it in the recipe to Infuse it later on?

Yes but you will lose the charr backpack skin

I would infuse it first, then put the charr backpack skin over it just to be safe and avoid buying another charr backpack skin.