Primary portal refers to the default portal the operator is logged into, whilst secondary portals are alternate portals which can be switched to if necessary. It does not ncessary mean the Designer Studio or Case Manager portal. If you view the Access Group record (Definition tab) you will see a list of portals defined:
Here we see two listed. The one with the radio button selected (Developer = Designer Studio) is the default one accessed when you login and is termed the Primary portal. The other (pyCaseManager7 = Case Manager) is the Secondary portal. You can switch to another portal from the Launch menu on the header.
So any Portal rule may be defined as the Primary or Secondary. There most be one primary and zero or more secondary portals defined for an access group.
Note whilst we do focus on Designer Studio and the Case Manager portal in Pega 7, the are in fact others available. For example the is the Access Manager portal (pyAccessManager) as well as others.