Maybe things have changed, but I'd say onions grown from sets normally split into several bulbs. It is natural.
This is only true for Shallots - 'normal' onions just give you 1 bulb per set planted.
At the end of their growing season onion leaves turn yellow and flop over. Leave them for another 2 weeks or so, then take them out for drying.
Agree with this bit - the stems will fold over by themselves (unless the bulb has developed a thick neck and these won't fold over). Some people like to pull them out of the ground and leave them on the soil surface with their root side facing the sun - said to help 'ripen' them so they store longer.
If its wet weather when its time to pull them up, then wash off any soil and leave them somewhere to dry off properly (greenhouse staging is good for this). Discard any dry/mouldy leaves - taking care not to damage the main bulb when pulling them off. Then put them in an old carrot sack (or similar) and hang then somewhere cool, dry and with good ventilation. This way they will keep right htrough the winter.