The From 1 is an application to make, you can certainly change your mind. The ATF requests that if you do make a change (and not a temporary one, but permanent one) you write them to notify the of said changes. Most people will consider an SBR lower a SBR lower, and any different uppers you put on are basically "accessories." The difference though comes in when the registered part is actually the upper (such as a SCAR) or PS90.
You can order the parts at any time. If an ATF agent randomly stops you on the street and you're carrying a complete lower in your backpack with a complete upper, it may present a problem. It's mostly common sense... if you had the complete upper I would just store it in a different spot, or keep the box sealed. Worst case, you just want an argument that you were not intending to put them together before the Form 1 was approved.
Think of it like this--- your cat gets sick and you have to give it meds. The vet gives you a syringe to inject the meds. If your syringe is in the bag with cats medication in the drawer at home, you're probably just fine. If for some strange reason you take the syringe and put it in a bag with some cotton balls, a spoon, and some strange white cleaning agent in a small bag then get pulled over--- you're probably going to jail. It doesn't mean you did anything illegal, you just made a real dumb decision to make it appear like you had the intention or you were doing drugs. Same logic applies, just use some logic. Say, lower in the safe and the upper in a different room in the top of the closet or something in a taped up box.