You choose how many targets Biogenic Upgrade has and how the counters are distributed as you cast it. Each target must receive at least one counter. This means, for example, that you can't target three creatures and assign them two, one, and zero counters.

If some of the creatures are illegal targets as Biogenic Upgrade tries to resolve, the original distribution of counters still applies and the counters that would have been put on the illegal targets are lost. They won't be put instead on a legal target.

To double the number of +1/+1 counters on a permanent, put a number of +1/+1 counters on it equal to the number it already has. Other cards that interact with putting counters on it will interact with this effect accordingly.