Once it’s calibrated you just have to send it a C (or whatever) from the MIDI and use the pitch knob to tune the oscillator to actual C. From there on the MIDI notes should be in tune — well, more or less; analog oscillator pitch does drift, so you will need to retune (with the knob again) at times. But the calibration should be good long term.
Also, there’s a known quirk of the 3340 where if you change the pulse width CV it changes the tuning. There are fixes for that though (and maybe you haven’t even included the pulse width control in yours in which case it’s not a problem).