Waddoups ordered that Breck England's name be placed on the ballot for the district that covers Davis County, and that Pat Rusk's name appear on ballots for the west side of Salt Lake County, including sections of West Jordan and Taylorsville.
The two candidates sued after they were rejected by a committee appointed by Gov. Gary Herbert or by Herbert himself, in a process that Waddoups said denied candidates their constitutional right of free speech.
State Elections Director Mark Thomas said clerks in Davis and Salt Lake counties have time to print ballots and send them out by Sept. 20, the deadline for mailing ballots to service members and others out of state.
The ruling on the board's election process comes amid allegations of dysfunction among board members and the departures of both Superintendent Martell Menlove and deputy superintendent Brenda Hales. Last month, Hales stopped working, saying she would use vacation and other leave until her retirement becomes official at the end of the year.
Shortly after that, Menlove, who had previously announced his retirement, decided he would leave rather than wait for a permanent replacement as he once planned.
After Thursday's hearing, England and Rusk said they would begin campaigning, though both said they didn't have a campaign organization in place.
"As a matter of fact I think the first candidate forum for me would be tonight," said England. "I'm going to be there. I'm going to ask to be heard."
The committee appointed by the governor selects at least three people per district from among those who applied to be candidates. The governor then chooses the final two whose names appear on ballots.
Before ordering that the two appear on election ballots, Waddoups raised the question of whether it made sense to do so, given that he had declared unconstitutional the selection process.
"If this [statute] is unconstitutional, it is void," Waddoups said. "If it is void any election attempted to be carried out under this [statute] would not be in force."
In last week's ruling, he found the process restricted speech because the committee and governor could make their decisions based on any criteria. That could mean certain candidates are excluded because of their views or could cause them to suppress certain positions in order to pass muster, he said.
Before the hearing, attorneys for England and Rusk and those representing the state reached an agreement to place them on the ballot. But Waddoups initially balked because of the bigger question of the effect of his previous decision.
Alan Smith, one of the candidates' attorneys, cited various cases in which judges had ordered names placed on election ballots.
But Waddoups objected that those cases might be too different because "they don't invalidate the entire election scheme, which is essentially what my ruling does."
Smith replied that no party was before the court claiming that this year's entire board election was invalid and that his clients were only asking that their names be placed on the ballot.
Assistant Attorney General Thom Roberts, appearing for Herbert and Lt. Gov. Spencer Cox, also told Waddoups the hearing called for a narrow ruling.
While his clients got to be on the ballot, Smith also said the lawsuit was not over. The complaint seeks a permanent injunction stopping use of the selection process.
Ultimately though, Waddoups said, fixes to state law "should be made by the state Legislature and not by the court."
Carmen Snow, a Washington County resident, also is a plaintiff in the lawsuit but she was excluded from the ballot in the 2012 election. She wasn't seeking to be placed on this year's ballot.