The Senate yesterday went along with President Carter on one issue - the B1 bomber - but at the same time was moving toward crossing him on another - the controversial plutonium breeder reactor at Clinch River, Tenn.

By 58 to 37, the Senate rejected a House move to spend $462 million to build fifth and sixth prototype of the controversial low-level "penetration" bomber. Four of the planes have been built, but President Carter last year terminated the production program in favor of the air-and-sea launched cruise missile. The B1 fight now returns a second time to a conference committee, where yesterday's Senate defeat is likely to be sustained by the House.

The $462 million voted down by the Senate for the B1 was the only item in the $7 billion supplemental appropriations bill for the 1978 fiscal year that divided the House and Senate.

Included in the $7 billion are funds for indochinese refugees, electric cars, synthetic fuels from coal and $80 million to continue the plutonium breeder reactor at Clinch River. President Carter has already vetoed an $80 million authorization for Clinch River but the House and Senate went ahead and passed the $80 million as appropriations for the same project.

"The comptroller general has already ruled that the $80 million appropriated for fiscal 1978 must be spent or it will be a violation of the law," said Rep. Mike McCormakc (D-Wash.), a key figure in the breeder battle on the House side. "It's just like the old impoundment business; if the president does not continue Clinch River, we'll have to take him to court just the way we took Nixon to court when he impounded authorized funds."

Even as the battle over the $80 million in appropriations heats up, a new one is about to begin over the $33 million President Carter has asked for in authorization money this coming fiscal year to close out Clinch River. The $33 million would do nothing more than pay contractors to terminate the entire plutnium breeder program.

"I don't think there's a whole lot to be gained by fighting this battle every year but I think we can win the next round on the breeder," said Rep. Walter Flowers (D-Ala.), chairman of the House Science subcommittee on fossil and nuclear energy research. "I'd prefer the president to support Clinch River, but if he doen't we're prepared to fight him and maybe even squeeze him a little bit to get the project underway."

Nowhere in the House and Senate is it clear as to what strategy will be used to "squeez" Carter on Clinch River but pieces of it have begun to emerge. The strategy is being helped by a strong lobbying effort by the nuclear industry, whose reach extends into the districts of as many as two thirds of the members of Congress.

Today, there are operating nuclear power plants in no fewer than 25 states. Only five states do not have some type of nuclear facility inside their borders and the environmentalist group Clergy and Laity Concerned said that counting nuclear weapons design and deployment there is not a single state untouched by the nuclear industry.

One of the strongest lobbies on Capitol Hill is Westinghouse Electric Corp., which has built almost half the nuclear-run facilities in the United States and is prime contractor for Clinch River. Westinghouse has carefully pointed out that 25 percent of the hardware needed to build Clinch River is built, half the $2 billion needed to construct it is spend and as much as 80 percent of the hardware has reached final design.

"We've compromised with the president and agreed not to break any ground but the clock is ticking away," Flowers said, "Every month we delay Clinch River we spend $13.5 million on carrying charges alone."

Another aim of the pro-breeder forces on Capitol Hill is to punch a few holes in the White house argument that the breeder is unnecessary because there's enough uranium in the United States to fuel the nation's nuclear powerplants for the next 30 years. The argument for the breeder is that the plutonium it "breeds" is an essential fuel because there isn't enough uranium to do it alone.

The White House says there's 3.8 million tons of uranium inknown reserves and unknown "resources" in the United States. An unpublished study by the National Academy of Sciences questions that assumption, saying there may be as little as 1 million tons and no more than 1.8 million tons of uranium. McCormack says that if that's true a nuclear power industry without a breeder will be shut down beforre the year 2000.