If you have some JavaScript/Custom CSS that you need to apply for your Office365 site, you can easily do this using the Custom JavaScript/Custom CSS feature in the Theme Builder tool by following these steps.

Step 1: Open the Theme Builder

Go to the Site Settings

Then to ShortPoint Dashboard

Click the Theme Builder option:

Select Customize my site button

Step 2: Apply your Custom JavaScript/Custom CSS

Once the branding & customization tool is opened, Navigate into Utilities

Then to Custom JavaScript or Custom CSS: 

Paste your code into the Custom JavaScript/ Custom CSS Field, and click Apply button: 

Custom JavaScript:

Custom CSS:

Don't forget to Publish your changes, so they will be applied on your SharePoint site.

Related articles:

Apply Custom CSS from ShortPoint Theme Builder