A CK2 title is converted to an EU4 country only if:
It is at count tier, or it de facto contains at least one de jure count-tier vassal title; and
It has no liege title; or
Its liege title is not among its de jure liege titles; or
Its liege title has an elective succession law under which the electors get their votes from their titles (not from their dynasties or their appointed positions).
A CK2 ruler is converted to EU4 as the ruler of the highest title that (1) he holds and (2) de jure contains his de facto capital.
For example, if William the Bastard holds England but has his de facto capital in Normandy, in EU4 his primary title is Normandy, under which England is in personal union. In order to make England his EU4 primary title, he must move his CK2 capital into its de jure territory. (The corresponding decision in EU4, to reverse the direction of a personal union, definitely needs to be implemented. See the case of Portugal and Brazil, as well as that of Brandenburg and Prussia.)
CK2 counties controlled by vassals inferior by 2 or more tiers → EU4 provinces in states; CK2 counties controlled by vassals inferior by only 1 tier → EU4 provinces in territories and controlled by estates
An EU4 province that is neither state nor estate is de facto independent and anarchic, and should either secede or be conquered by a nearby estate (or by the central government, or by a new grassroots local estate) in the long term.
No EU4 province can be both state and estate in the long term—the central government is an estate all its own. If this situation occurs in the short term, it should represent ongoing struggle between the central government and the estate for control.
(Is this too similar to M&T? I can't remember, desu.)
This is meant to match how an EU4 country magically gets a boost to its state cap when its tier rises. I would prefer to make demesne counties correspond to state provinces, but it just doesn't match.