Thank you Stonysmith.
After several hours of furrowed brows and quite a bit of swearing I was able to successfully acquire an access token and secret.
Some things I realized:
1) Since I logged in as myself on Shapeways, then registered for an App ID. The consumer key and consumer secret will be associated with my login and the things I upload using the php scripts will show up in my account. So this actually answers my original question. I was thinking that registering for an App ID would create a separate place that the model's would be uploaded which would complicate things. This is not the case and the App ID uploads to my Shapeways account.
2) The sample php files provided in the Shapeways php-pecl directory are not actually websites I can plug into the browser bar but instead interactive command line php scripts which prompt the user for values. This is an important distinction. The php doesn't wait for the user to plug in the PIN value when I was running it from the browser, so I kept getting access errors.
So to summarize my use of the php-pecl scripts:
1) Login to Shapeways with your username and password.
2) Create a new App (IE fill in all the required blanks) and then push the "Create App" button.
3) The Shapeways Developers website will provide a consumer key and secret token. Plug these values into the "consumer_key.php" file.
4) Run the Authorize-oauth1-pecl.php script using the php command line. On my mac this command looks like this:
php -c <long_path_name_to_the_php_ini_file>/php.ini -f Authorize-oauth1-pecl.php
4) The Authorize-oauth1-pecl.php will talk with the Shapeways servers using the consumer key and secret token and return a URL that the user is to cut and paste in the browser to get a PIN number.
5) Take that pin number from the generated URL and plug it into the "Pin: " prompt from the Authorize-oauth1-pecl.php script
6) With the correct PIN entered, the script will provide an access token and secret which the user can place in the "access_token.php" file for use with the other scripts in the php-pecl directory.
I realize I'm being very verbose about this, but I'm writing this down to help others and so that I don't forget. These instructions also assume the user has successfully installed php, php-pecl and oauth modules. I might add these steps also required quite a bit of swearing.
Thank you again.