shaolindoman, to be blunt, it also sounds like you are new to e-commerce. You are raising significant issues, important ones, but thorough answers are beyond the scope of a single reply. Here's some starting points:

First, I need to develop a way for users to login to my site, yet restrict access to certain parts (I really don't want to use cookies but if need be then so be it)

Super Search PM for topics on passwords (here's a taste and ways you can handle them. Some use cookies, some use a database like MySQL. But to restrict users to particular areas you will probably need to develop two levels of navigation, and either be checking the DB or cookies as they move from page to page. Using the database for users and passwords will also answer your last question. MySQL has an encryption feature, but you can look at modules like Crypt::CBC and many others.

Second, I also am developing a checklist shoping cart. I have a crdit card validator right now, but I need a way to encrypt the numbers and send them over as well as other personal information in a secure manner

You need to have a secure certificate (like Verisign) filed with your host (they do the encrypting). However your credit card validator's gateway will require a rigorous protocol for authenticating user info—and all of them are a little difference. So, to answer your question, much of this is handled by virtue of the fact you have followed standard e-commerce procedures.

There's lots of reading out there. Good luck.