As the wikipedia entry well explains,
There are two main variants of
inverted indexes: A record level
inverted index (or inverted file index
or just inverted file) contains a list
of references to documents for each
word. A word level inverted index (or
full inverted index or inverted list)
additionally contains the positions of
each word within a document. The
latter form offers more functionality
(like phrase searches), but needs more
time and space to be created.
Since you don't tell us which variant you have, we can't really answer your question precisely, but thinking about each possibility will help.
To open and search documents is typically a costly operation, unless your documents are unusually small, so you want to minimize that -- and option (2) doesn't really minimize it. If you have an inverted list, with option (1) you won't even need to open any document; if you only have an inverted file, you'll inevitably need to open documents and scan them (since you otherwise lack information to confirm word adjacency) -- but at least with option (1) you minimize the number of documents you have to open and scan (only those in the intersection of the lists of documents containing each word).
So, in either case, option (1) is more promising (unless your documents are peculiarly small).