Yes it is technically 2 cells, but when connected in parallel (and the battery's are the same) it is a big 1-cell battery, multi cells like 2 - 1000 cells in generally a term for a battery with more voltage, like a car battery which is a 6-cell battery (2V x 6), if we use a 2-cell Li-ion battery then it would be 7.4V not 3.7V
The voltage in the 2 battery's is not critical when connecting them together, meaning that if one is 3.7V and the other 3.9V then it would be ok, just don't go much "higher" then that, and this means not more difference then 0.2V between them
So it does not matter if they are 3.3V or 4.2V, the way i do it is just charge them both up to 4.2V.
Again just don't connect 2 battery's with a high voltage potential between them, like connecting a 3.3V and 4.2V this has a risk of damaging the battery's, and if you do this after the circuits it could destroy the circuits.

Connecting the battery's after or before the circuits should not be critical, use zimon or cantruchd mod if you prefer a less "destructive" mod
I posted the links in post #2