Charging a battery with two sources, should I put them in series or parallel?
It's better to use just the generator so you don't have to tolerate the variability of the PV.

If, when fully charged, each cell is at 1.2 volts, then you'll need a current-limited  source with greater than a 3.6 volt output to charge them, the current limit being determined by the cells' specifications.

If your generator can't generate more than 3.6 volts, then the PV should be connected in series with it. 

Unless there's some compelling reason to do so, the PV and the generator shouldn't be connected in parallel, directly, since the one with the higher voltage will feed current into the one with the lower voltage, possibly starving the battery or increasing its charge time.

Also, since more voltage will cause more charge (current) to flow into the battery, it's better to arrange things so that the charger's output voltage only pushes the allowed current into the battery.  That is, neither excess voltage across nor current into the battery is a Good Thing.