If a file is still beneath the /concrete directory, it will be lost next time you update /concrete.
The only place it will not be updated except by you is if you work in either of
- your own package beneath /packages
- beneath /application
The purist approach would be to clone Atomik. But that can become quite a major hassle and requires some developer expertise.
The quick and dirty approach is to continue as you have done, but also keep a copy you can re-apply immediately after any core update. You just need to remember what needs doing, or document it thoroughly if someone else is likely to be doing future updates.
Another approach would be to use a marketplace theme that has the layout you want. Most marketplace themes have a bit more flexibility.
A fourth approach is to create a shim theme. A thin layer of theme that provides your extras, but mostly just pulls in Atomik. This requires a bit of developer expertise in a different direction to cloning Atomik, but is generally quicker than messing with Atomik directly.
A slightly hacky approach would be taking advantage of a quirk of the core. That once a theme is installed and activated, its templates remain available to the active theme even after your new theme is no longer active. You can use this trick to piggy back templates from your new theme onto Atomik. Create a non-entity theme with your templates (named differently to Atomik templates). Activate it. Then re-activate Atomik.
A very hacky approach would be to use some JavaScript to modify Atomik when the page is viewed (but not to mess with edit mode).
So overall it depends on your ability with code, how much you want to do (or pay) now, and how much of a legacy of work you want to leave for the future.
If you want an easy life, find a suitable marketplace theme from a reliable marketplace developer. A few dollars now will be money well spent.