Open up your Incarnate window on your level 50 character. Have you unlocked your Alpha yet? If you have, you should also see you have earned threads in your salvage window. Take a look at all the Alpha power options and decide what's best for your character (for example, many of my melee characters go with Musculature - we love more damage!). Ignore crafting anything with shards as that stuff has been disabled. Only concern yourself with earning Empyrean Merits and Threads - that's what you use to craft all your Incarnate stuff.
The way the people who wrote the Incarnate guides got the knowledge in the first place was by rolling up their sleeves and jumping right in. So that's my recommendation. There's a huge difference between a level 50 character and a tier 4 kited out Incarnate. HUGE difference.
Login in your favorite level 50 and unlock Dark Astoria by talking to Captain Nolan (if you're a hero, can't recall the villain contact). Finish his missions and you'll end up in Dark Astoria where some of the good contact Incarnate missions are - run through those, earn levels and unlock all of your slots. Then you choose what Incarnate slots you want to craft to better round out your character.