Hello InkGIRL, and thank you for your question.
You can use a temporary URL while your domain name is not currently pointed at our name servers yet. You can read our guide on testing your website using your temporary URL for more information on this.
When you're ready to use your domain name instead of a temporary URL, you'd then want to update your domain's name servers to point to ours. That way when someone types in your domain name, it pulls from our web server.
If you aren't yet ready to point your domain name to our name servers, and would still like to test with the actual domain name instead of using the temporary URL, then you'd want to modify your hosts file. This forces your computer to resolve your domain name directly to our web server.
Changing how you access one domain on your account over the temporary URL shouldn't affect the others. For instance if you had /~userna5/siteone and /~userna5/sitetwo as temporary URLs, then you created an Addon domain for siteone.com pointing to your /public_html/siteone/ directory. You would still be able to access /~userna5/sitetwo without any problems.
Please let us know if you had any further questions at all.
- Jacob