I'm in the process of setting up my new "Weebly" Square store. It leaves a lot to be desired as far as customization goes for now... I do hope they start to add more features like WP style theme installs... but they have not, yet.
For now, you can only change a few things.
Background images: You can change the background image in the editor under the "Section Style" option on any given section. E.g. "Page: Home" click "Header" then open the "Section Style" and there's a drop down to apply an image. The image will persist on any page that calls that section. You can create multiple sections if needed, but they cannot be applied on all pages (e.g. Category Pages)
Fonts:
Font defaults are set on the editor's menu (left side of screen) at the bottom under the button titled "Site Design". You can change the default theme colors, fonts, etc.
Fonts can be set on a block by block basis. Click the section you want to edit, then click the text block to see font options.
