Hi,
Yes you can insert code in a custom.css file of your template, but if you edit the frontend css file of HikaShop via the menu Configuration > Display > CSS, when updating the modifications will not be lost too. 
Regarding the layout of the quantity field, the view to edit is "product / show_quantity".
We already have many options for different layout of the quantity field, so what can be done is to edit one of them as you want.
And you can select the quantity layout in Configuration > Display > Product, of in the category or product edition pages.