Simply you can't.
We have taught about it a lot and couldn't find a way out. Unfortunately if you make some changes (especially with php files) then once you update, your changes will be retrieved back to stock. Because CleanMart works based on files.
But; about the CSS file, it is relatively easy. We are putting the additional lines to the bottom (and we don't change the above) so, basically get the v1.2 and open the flexibleVM2Global.css, scroll to the bottom and find this line:
/*
---------------------------------------------------
CleanMart v1.2 -- The CSS lines for CleanMart v1.2
---------------------------------------------------
*/
Copy the CSS rules that stay below of that line and paste them to your flexiblevm2Global.css so you won't retrieve your changes.
But this is not possible with the PHP files. You need to re-do what you have done to get your modifications back for PHP files.
Regards,
Support