It just means you’ll have to write your own ADC code, which is not terribly difficult. I’d recommend changing PA3 to PA4 (ADC2_IN17) or PB2 (ADC2_IN12) so the second motor can use all ADC2 channels to keep the code cleaner. Channel numbers don’t need to be consecutive or ascending order or anything, the sequence registers can convert them in any order you like. The only limitation is that in dual mode, ADC1 and ADC2 can’t convert the same channel number at the same time. But you shouldn’t have to worry about that. Read the ADC section in reference manual rm0440. There are also a couple of RCC bits you have to enable at startup. See my code here, although I haven’t actually verified that it works yet: Gooser: a 4-in-1 Lepton derivative - #21 by dekutree64
Yours will be simpler in some ways since you don’t have linear hall encoders mixed in, and won’t need dual mode. Just set them up independently to read their 3 channels when triggered. But also more complicated that you’ll need to figure out how to trigger it off the timer for low-side sensing, unlike my inline sensors where I can just set ADC_CR_ADSTART from the main loop.