Maybe I should post here few hints to help you to use the features better
If you already have some accounts set in the submitter, let's say before your first use of the PA requester, click on the Import Accounts button (in CPAR > Step 3) to import them into the requester. Apart from importing your login info their status will be changed to Approved what also means that these sites will automatically be skipped from generating in the requester (there's no need to apply for new partner accounts if you're already approved).
Once they are imported do the rest (generate new sites, request, etc.)
Use the Export Accounts button when you wish to export your partner accounts set in the PA requester to the submitter - either all of them (leave all rows unselected in Step 3) or only the selected ones.
If you are not sure how that exactly works I do recommend you to try that out on some selected sites - e.g. select 2 of them and hit Import or Export etc.. and check their settings in the submitter as well...
Also, don't forget to check the Help files included in both softwares (Help menu > Help) as well as the interactive tutorials available on
http://www.chameleonsubmitter.com/tutorials.php