It didn't work that way. The Soviet Union did not have a market economy with state owned enterprises. Its economy was a planned command economy which utilised the material balance planning system. You may read to last paragraph for tl;dr.

Briefly, the Soviet economy was administered by an agency called the State Planning Committee — Государственный комитет по планированию, or Госплан, for short. We'll use English, and call it Gosplan.

Every five years, Gosplan created a plan for the next five years (Five year plans), which was usually quite broad. It would have to decide if it wanted more capital goods (things that help you make other things) or consumer goods (stuff we buy to use). The prices available to the public were set at rates relative to incomes, and industry had to keep up to make enough stuff. This is the "planned" part.

Let's take a random, created example: Gosplan wants a factory to make 500 more cars per year. So they need 500 more engines, 2,000 more wheels, and so on. The factory is given the command to make 500 more cars. It will be supplied with all the things it needs from other factories like motor factories, leather for seats, and so on. Those factories do not choose what to do but are instead told what to do by government bureaus under the aegis of Gosplan. This is the command part, and Gosplan is the commander (mostly).

As you can imagine this is quite complicated. Everything must be worked out in terms of inputs. If you want 500 more cars, you need at least 500 more tonnes of metal. So on and so forth. Gosplan did have financial account sheets (I won't go into this here, but it was not same as our UN system of national accounts, Communists had slightly different one) but it also had to keep track of every type of produced thing. This is called material balance planning.

Factories weren't profitable, and were not intended to be. They didn't sell things at a higher cost than it took to make them, but instead produced goods in accordance with a larger output plan. They would go on working and the state would go on paying the workers, even if it wasn't efficient enough. But if they couldn't make enough stuff, there simply wouldn't be enough stuff in the shops for workers to buy. Gosplan didn't control the whole economy of USSR. There was always allowed a little bit of private activity. But basically, that's how the system functioned. No matter what, the state continued to pay workers in cash for goods whose price was not dependent upon their supply.

edit: soviets themselves used capital to output ratios (ie what did fixed plant produce relative to how much it cost) as a basic measure of what we might call "profitability." the return on investment ratio was important to communists. russian term is Фондоотдачa (fotdootdacha).