With single purchase of any product, you are licensed to use the product on one store only. If they are running several stores on a single PrestaShop installation with prestashop's multi-store feature, you need to purchase a separate license for each store.
It's okay for you to use your theme on a development site, two ways to do that.
1. Put the development site in maintenance so you can use all features with out registering it.
2. Register your theme on the development site so you can use all features, when you finish setting the site, de-register it first, and then move the site to a live server, so you register your theme again there.