I've usually treated them as "rivals" - not actually enemies but definitely not friends either. They are competing against each other for leadership of the nation and could be viewed in simplistic terms, as two different political parties competing against each other - not enemies, not friends, they are rivals.
But this gives you a lot of opportunity to vary the relationship in different parts of the country. In some areas they may actually be friendly with each other and even offer limited assistance to each other. In another area they may not actively assist each other but they don't actively interfere with each other either, an "uneasy alliance" against a greater enemy sort of situation.
In other places they may be directly competing against each other for resources and so they do come to blows every now and then and in some locations they may be actively seeking to eliminate each other.
A lot of this comes down to the type of people in charge of the local groups. Certain personalities might only be interested in promoting their own group's welfare and thus consider the other 'gov' not just a rival but a potential threat. In some locations the leaders of the local groups may actually be friendly and may promote working towards common goals rather than fighting among themselves.
It does mean more book-keeping for the Referee but it makes the situation between MilGov and CivGov a lot more dynamic and makes it feel 'alive'. The PCs will not know how the two 'govs' relate to each other in a particular region without getting some intel, or going to see it for themselves. It also means there are great opportunities for the PCs to act as intermediaries and even peace-makers between the two 'govs'.
For me, this sort of thing makes everything a lot more interesting.
The PCs become troubleshooters and even diplomats for the greater good of the USA.
Promoting the idea that MilGov and CivGov are Americans and they should work together to promote the recovery of America for all Americans - there's a long term campaign in that!
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