Hi Pete,
Yes, when your main portal is fully configured as you would like it to be, go to Host, Portals and export it. Then when you create a new portal, the exported one will be available on the templates dropdown list.
The option to "export content" with the template can be useful if for example you want to set up some text modules with useful content ready to go. Not all modules support this however and you will need to test yours to see.
If you export with content, you will get two template files. The one with the content is a zip file of the portal folder - just add .zip to the filename and you can look inside it. Content in a text module is not in there, and is instead in the other file. You can open that file in notepad or an XML editor and see what is does - it's strightforward and you can edit it by hand.
There may be a problem depending on what you mean by permissions being "shared between portals". The roles you created , and any permissions applied to pages or modules, will be exported in the template, but there is no role or permissions sharing across DNN portals - portals are independent websites.
If you need shared access (SSO) across portals then you will need to use a third party module or better, use a single portal and design a good role heirarchy instead.
Hope that makes sense.
Rob