You should contact your space host administrator(or search in FAQ). As me know, the php.ini should be placed in site www(site root) folder, but it depends the space supplier, some supplier don’t use php.ini. And, you need re-start PHP server after changing php.ini.
Yes, the changed theme file will be covered when theme updated.
– If you only change some style of theme, please go to Appearance > Customize, put your css code to “Additional CSS” box.
– If you want to change more codes. We strongly suggest you use the Child theme, put your own css/js/php file into child theme folder. Refer more about child theme