Can I use my account for more than one website?

We run a couple of different non-profits, can I use this account to make forms for both sites?

Yes, you can embed forms that are created on same account on different websites. 

This guide can help you to embed your forms to your websites:

Which form embed code should I use?

Adding a form to a web page

We usually recommend using of iFrame code: 

https://www.jotform.com/help/148-Getting-the-form-iFrame-code 

Hope this will help. Let us know if you need further assistance.