WITH THE RETURN to Florida of most of the boats that had gone to Cuba and with no new boats being permitted out, the "freedom flotilla" is on the way to being at least temporaily beached. Any resumption of the flow of Cuban refugees can come about now only through formal Cuban-American agreement, which, in the circumstances, is not likey soon. For that reason the pause is unfortunate. But it does provide an occasion to care more effectively for the 94,000 Cubans who have arrived so far.

The chief legal tool at hand is the Refugee Act of 1980. No one had really gotten the hang of this act before the Cuban exodus began; some now prematurely suggest the Cubans should be treated under special legislation. The act establishes two categories: refugees and those seeking asylum. Refugees are meant to be processed systematically overseas and, when individually approved, admitted to this country. That is the arrangement the United States would still like to work out with Havana. Those seeking asylum, on the other hand, simply appear in the United States, where their individual cases are reviewed.

Clearly, those who drafted the statute had envisioned Indochinese "boat people" in the refugee category and only an occasional musician or athlete in the asylum category. The Cuban situation fits neither box very well, since the American government was not able to screen applicants first on foreign soil. The question of determining the Cubans' status now has produced a nasty snarl among precisely those federal and indispensable private agencies that need to work together to make any program succeed.

To us, it makes sense to define the new arrivals as refugees. This ensures the administration the continuing consultations with Congress that, in a situation as delicate as this one, the administration should be eager to conduct. Moreover, given the intricacies of the Refugee Act, it will be easier to make a systematic conversion of refugees to permanent status for those who are allowed to stay in the country. There is no difference in the screening procedure and, notwithstanding some of the things you hear, no basis to the argument that one status or another will drive up the cost of the program.

Resettlement of such a large group will cost money -- money that is largely a federal responsibility to rpovide. This is a domestic cost of the country's foreign policy, and one that it has no real choice but to pay.These costs historically have been only transitional: Cubans in Miami, like virtually all other refugee communities, benefit the economy once the initial transition is made. For this reason as well as for the more obvious one of honoring commitments already made, the unexpected arrival of the Cubans is no excuse to reduce either the number of Indochinese refugees already planned for this year or the funds to help them join the mainstream.

Ideally perhaps, the flow of refugees to the United States -- as to other nations -- would be dealt with through the U.N. Commission on Human Rights. But in the short run, for both humanitarian reasons and efficiency's sake, the United States' own system must be made to work well.