President Reagan's new Bipartisan Commission on Central America begins its work this week. If it is well organized and fulfills its mandate as promised, it will perform a singular service to the country. Not only do most ordinary Americans not understand what is going on in Central America. Within the US government itself there are wide divergencies of opinion over US policy. Taking a studied look at the whole question, the commission may be able to clarify issues and recommend a long-term strategy which makes sense to the American public and wins bipartisan support in the US Congress.
There are, of course, misgivings about the commission. Its composition is weighted on the conservative side, and at the moment there is ambiguity as to whether a liberal member of the panel will stay on. The member, Cuban-born Yale economics professor Carlos Diaz-Alejandro, was sworn in Wednesday along with others, but the White House says he serves on a ''contingency'' basis pending a background check. Certainly the President would risk losing credibility if he bowed to the pressures of conservative Cuban exile groups to remove Mr. Diaz-Alejandro.
Then there is the issue of Henry Kissinger, the panel's chairman. The appointment was made without consulting Congress and has furrowed eyebrows among Democrats and Republicans. Aside from controversies over his past management of foreign policy, Mr. Kissinger evokes concern just by his high-powered style of operation. When he moved into the State Department the other day, he was confronted by a battery of television cameras - more than accompany Secretary of State Shultz. Mr. Shultz, fortunately, is not a publicity seeker, but Mr. Kissinger nonetheless will have to take care to keep a low profile so as not to eclipse the secretary. Otherwise US diplomacy could suffer. To many at the State Department, this all looks disturbingly like a replay of the days when Mr. Kissinger captured US policymaking from Secretary of State William Rogers.
However, Mr. Kissinger has sought to alleviate worry that he will jump into the day-to-day operation of Central American policy. ''I am not taking over Central American policy,'' he declared recently, though he has not denied that his advice is frequently sought by the White House. He has also given his assurances that the commission will hear out the views of every significant group. There is no reason to think he will not follow through, knowing as he does the political uproar that would arise if the panel and its method of operation did indeed turn out to be ''stacked.'' Much will depend, too, on how hard such panel members as Rep. Michael Barnes, a critic of administration policy, press a thorough investigation of opposing views.
When the commission reports early next year, it can be hoped it will be able to outline those ''political, economic, social and security goals'' which the US should pursue in Central America over a long-term period. The US has had a long history of intervention in the region. Even now the administration is stepping up military force there, prompting many Americans to wonder if the outcome will be any better than it has been in the past.
What Mr. Kissinger can bring to this important task is his keen historian's eye and his ability to analyze the various forces and factors which impinge on a situation like this. How big a stake does the Soviet Union have in Central America? To what extent does the crisis have indigenous roots in social inequality and economic disparity? Is it possible to solve the problem of creeping Marxism by military action? Would massive economic development aid for the region serve to build more democratic rule? Or is it imperative first to stabilize the area politically and reform the social structure? How can that be done without bringing in leftist political groups? What is the United States's strategic interest in the region?
These are but some of the questions which will confront the new presidential commission. If Americans are to sustain an indefinite effort to help ''democratize'' Central America, they will need to know the answers.