Community Store how to use theme?
*Sorry if this should be posted on Github, I've seen a few forum posts about it on concrete5.org*
I've used Community Store on a few projects lately with custom themes and I've not had to do anything to apply the theme to these pages. I can also change between themes and the cart and checkout pages update accordingly.
The only thing I can think of is that maybe your theme doesn't have a view.php file in it?
In your case, it is just using Elemental on the checkout or are you getting just the checkout fields and pretty much no styling?
Any coding errors in the view file?
Any errors showing in dev console?
Any html errors when viewing source code?
If you use a 'Bootstrap' theme you shoudn't need to move/copy 'checkout.php' to the app folder.
Same as clients not seeing updates to website when forgetting to refresh browser!