Hi, i am not support rep, but a user like you. Custom capabilities (ccaps in short) can be used in two main ways:
1- you can enter the ccaps (whatever word you want to use is fine) in the top right box where you see “Require Custom Capabilities?”
This will make the whole page unavailable for any user who does not have that ccaps access.
2- you can use it with conditionals, where you can show part of a page for those who have specific ccaps, and other content for others.
Then, you have to assign the ccaps to the user mainly with the buttons or pro-forms, when a member registers (i think you can assign ccaps with free registration, but i am not sure how, since i dont use it myself).
For an example, on my site (http://scrapbookcampus.com), members can be given the ccap “basic” if they purchased the Basic course, and the pages with the various lessons are protected with that box (on top right). I am also using ccaps for various workshops i have: if the user does not have the ccaps for a particular workshop, they will see a “sale pitch”, but if they do have it, they will see the actual video and link to download the documentation. For the workshops, i have them assigned individually as wjan2012, wfeb2012, etc.
Hope it helps. If you have more questions, don’t hesitate to ask. Someone will surely be here to help.