THE TRANSITION, almost everyone agrees, is a model of smoothness and good feeling. Except in respect to El Salvador. There it is a mess -- there is difficulty in neighboring Nicaragua, too. First, people claiming to speak for Gov. Reagan spread the impression in El Salvador that he will junk the Carter effort to shape up the reformist junta of the center and will welcome a right-wing military coup. The American ambassador, outraged -- and with reason -- to find not only his status but American policy thus subverted, snapped back hard. Authoritative Reagan spokesmen, dismissing "pretend emissaries," have now denounced the terrorism of right as well as left and stated that "the alternative to the existing junta today is extremism on either side." Yet the roughness and bad feeling persist.

In fact, poor, little, terror- and war-torn El Salvador is caught in the mesh of two struggles. The one, the violence and maneuver at home, is about power. The other involves the policy argument going on in the American transition about how to address Third World change. In both, the current focus is on American aid to the reeling-but-still-ruling civilian-military junta. The Carter administration suspended the aid last week after a sequence of terrorism in which elements of the junta may have had a hand.

Many in the Reagan camp saw the suspension as a debilitating, self-defeating, human-rights gesture taking cards away from a leadership that, for all its failings, represents all that stands between Salvador and an eventual leftist takeover. Administration strategists, however, saw the suspension as a get-tough gambit meant to deal cards to junta moderates in their effort to bring junta right-wingers into line. If this is done, the theory goes, those moderates will be able to capitalize politically on the vast new American-sponsored land reform, and on improvements in public order, and prevent the country from going down the drain.

The war in El Salvador is grim beyond imagining. What strikes us most about the argument in the United States, however, is that once you trim away the ideological embellishments, administration and mainstream Reagan people end up agreeing that the junta is El Salvador's best hope. The real argument comes down to questions of tactics and timing: Do you help or hurt by jiggling aid? Is it enough for the Reagan people now to denounce terrorism or should they also endorse reform? Or is reform now irrelevant and armed struggle the only plausible way? Will the center hold until Jan 20? That last question is the most troubling one.