If you're going to use an existing lower...
1. Decide how you want to register the lower (i.e. individual, Trust, LLC, etc.).
2. Submit the Form 1 and accompanying paperwork to the BATFE.
3. Upon approval, engrave the lower with your Name, City, and State in a conspicuous location. There are legal requirements for the location, size and depth.
4. Order the SBR upper.
I've SBR'd two lowers and purchased a factory SBR and I would recommend getting a factory rifle, if you can. It is done on a Form 4 with all the pertinent info coming from the dealer making the paperwork a bit easier. You also don't have to engrave the lower. Just buy a factory rifle, sell the upper, and put on your choice of upper.
Whichever route you choose, I wouldn't recommend getting your upper until you've got an approved stamp as you've got a non-SBR AR around and that is bad juju.