PHP/JavaScript/MySql - Add Screens and Reports

I have created 2 sites. One is based in Drupal 6, and the other is a store front with Zen-cart. Both these sites are fine. I'm creating another set of programs right now to allow access to the posted zen-cart inventory for use by a rep or client. They will only be able to change their info. The passwords and login's will be controlled through the drupal site. Much of the programming on these screens is in JavaScript (Data Grids and File uploads) with php and mysql to load and save the data. What still needs to be done: setup a multi-layers access in Drupal (easy) to allow access to certain files based on login. Login to Drupal (also easy) do get access to the data base in Zencart using the programs I'm writing now. (don't know how to do this yet because I have not looked at how drupal uses cookies and logins) Finish all the rep/client screens. Print reports for reps and clients, HTML output or pdf. I'm looking for help on 2 items. Finish the site and site optimization when done with the coding.