You can connect a preamp into the aux input (or any high-level inputs) of an integrated amp. Just keep the volume control low so you don’t overdrive the preamp section of the integrated amp.
This is correct.
From what I understand, the impedance mismatch made the signal backfire into the amp and scarlet, frying them both.
An impedance mismatch would only affect sonics, if it had any effect all. It would not cause damage.
I could accidentally press the GAIN button on the atom amp and kill everything, so I would rather just get a new amp and be safe.
The high gain mode of the Atom provides a gain of around 12 db, which is perfectly reasonable for a preamp. Using that setting won’t hurt anything as long as the volume control is not cranked up too high. The recommendation in the manual to set the gain to low when using the RCA outputs is mainly intended to optimize the part of the volume control’s range that is used in typical setups, and perhaps also to optimize noise performance and sonics. And in some systems the low gain setting will not even be suitable when the RCA outputs are used, since that setting provides no gain.
Question: When you plugged or unplugged the cables connecting the Atom to the SMSL, did you have the components turned off? If not that is what might have caused the damage.