SECRETARY of State James Baker has landed his diplomatic jet in the middle of a furious sorting-out process in the old USSR.In the still-forming Commonwealth of Independent States, some republics (Russia) are stressing "commonwealth;" others (the Ukraine) are stressing "independent." Russia's Boris Yelstin would like to see a more centralized army with local militias in the states. The Ukraine's Leonid Kravchuk, who didn't run his election campaign on recreating a union, wants a small central force and a large Ukrainian army to be drawn from Soviet forces now on Ukrainian soil. It is important that Mr. Kravchuk not take such action alone - harming the Minsk accord that formed the commonwealth. Mr. Baker carries arms-control proposals he will validate through Boris Yeltsin. Nonetheless, he is scheduled to meet Mikhail Gorbachev today. Baker and Gorbachev have been waging a battle in the press, with the Soviet leader angrily telling Time magazine that Baker (and by indirection, George Bush) let him down by not supporting the union. Baker will undoubtedly tell the embattled Gorbachev, who may not resign quite as quickly as everyone thinks, that the Oval Office has been loyal almost to a fault - h aving been criticized for months in the US press for sticking with Gorbachev when it appeared, after the coup, that power was flowing to the republics. Baker will get an up-close view of the most interesting questions facing the new commonwealth: Who will belong to it and on what terms? For several years it's been said the Soviet Slavic republics would just as soon see the Asian and Islamic non-Slavs leave. Uzbekistan, Tadzhikistan, Kazakhstan, Turkmenistan, and Kirghizia have been a net economic loss for Moscow. These republics want to join the commonwealth. With the exception of Kazakhstan, half ethnic Russian and nuclear armed, Yeltsin may try to keep them out. If so, the Islamic states may threaten Moscow with a "Greater Persia" scenario - a link with Iran. It will be hard to exclude the old republics. What may evolve, though, is a "layered" commonwealth, with some republics more equal than others.