It is necessary for you to modify the workflows that are shipped as you have to adjust the urls to your specific site. There is nothing special about the workflows, so use standard CRM practices to adjust them.
You can also customize or add new entities.
Yes, you can include additional modify/add forms and control through different roles for administrators - just use the pages that implement case management as an example.
The portal framework is documented in the SDK, but the best thing is to examine the customer portal itself - we give you free source code just for that purpose. The code for the site is simple enough to be practically self-documenting.