It can join phrases or clauses. It always seemed to my (non-native Latin-speaking) brain that it should just be for joining two words, but I don't think there was every any justification for my thinking that way. Anyway, every time I would see it joining more than that it would strike me as odd.
Here's a quote from Bennett's New Latin Grammar:
-que is an enclitic, and is appended always to the second of two words connected. Where it connects phrases or clauses, it is appended to the first word of the second clause; but when the first word of the second clause is a Preposition, -que is regularly appended to the next following word; as,â€”
ob eamque rem, and on account of that thing.
It doesn't give any guidance about how frequently it would be used relative to other "and" words, but certainly it confirms that it is used for clauses and phrases. In addition, Bennett adds:
a) et simply connects.
b) -que joins more closely than et, and is used especially where the two members have an internal connection with each other; as,â€”
parentÄ“s lÄ«berÄ«que, parents and children;
cum hominÄ“s aestÅ« febrÄ«que jactantur, when people are tossed about with heat and fever.
c) atque (ac) usually emphasizes the second of the two things connected,â€”and also, and indeed, and in fact. After words of likeness and difference, atque (ac) has the force of as, than. Thus:â€”
ego idem sentiÅ ac tÅ«, I think the same as you;
haud aliter ac, not otherwise than.
so it's probably more the type of connection that the author wishes to convey that determines when to use each.