It depends on the VCO's pitch controls. In some cases, you have an octave switch and a tuning control, while others use the coarse/fine tune knob pair routine. The former (which began with Moog) can be easier to sort out, since these tend to use the tuning knob over a restricted range, either 12 or 24 semitones as a rule. The other method can be more of a pain...but also allow the VCO to get into frequency ranges that the octave switching method might not allow.
It's worth noting, btw, that if a VCO has NO fine tune control, it's apt to be a real pain to use in a precisely-tuned manner unless it's part of a set of VCOs under a single control set.
As for how I tune, I do it by ear. This is what I recommend, actually, as it helps to increase your pitch acuity over time. The better you can recognize what "in tune" vs. "detuned" vs. "out of tune" sounds like, the quicker you can work and the quicker you can realize when retuning is necessary. I really only use a tuner when working with microtonal intervals...which brings us to...
Quantizers. Now, these do NOT help with tuning. Quantizers are designed to force an incoming CV signal into scalar intervals which can then be used to control VCOs, etc. But they won't help keep the VCOs in tune, they just make them play pitches that conform to the quantizer's scalar parameters. It's still possible to have several VCOs that are totally out of tune with each other, but tracking the same scalar "pitches" equally (which can sound interesting in of itself; see Aphex Twin's "180db_" on "Syro").