Item 4c on the Form 1 should list the caliber you plan to initially build your SBR. So, if you're going to build as 5.56, enter (only) 5.56 (don't enter 5.56x45). If 300 BLK, enter 300 (with no leading decimal). There is no need or benefit to attach a letter or other document detailing other configurations you may want to use. This is distinct from the marking requirement.
An SBR must be "conspicuously marked" with its caliber. That marking can be on the receiver or barrel (or, I think, a few other places; I don't recall what they would be though). The marking needs to reflect the actual caliber. So, if you're planning on a 5.56 build, you could engrave your lower with "CAL 5.56 MM", and you'd be fine without having anything on your barrel. However, if you put a 300 BLK upper on it, it would need to have the caliber marked in a place that was visible without disassembling the gun.
ATF requests, but has no legal basis to require, that you notify them of any "permanent" change in configuration of a NFA weapon. In the case of an AR, it's pretty hard to argue that anything is permanent, particularly when swapping uppers.