Under US rules the primary of a wye-wye transformer must have the primary neutral connected to the supply neutral. This is to prevent parasitic overvoltage due to 3rd harmonics and slight differences in the magnetizing current of each phase of the transformer. If the secondary is used as a grounded wye system then normally both neutrals are solidly bonded together.
An abnormal situation would be a dairy farm where the primary and secondary neutrals would be connected together using a 5 KV class lightning arrestor or inductance. The 2 neutrals then use 2 separate sets of grounding electrodes that are say 20 feet apart. At the far end of a long distribution circuit the voltage drop in a perfectly good primary neutral is enough to cause a step potential that would bother cows. When cows are being milked the situation is similar to how I got a nasty shock form picking up a 1.5 volt dry cell by the ends - I had let too much perspiration salts build up on my hands. Cows do not like the Cow Voltmeter Method.
However, sometimes a wye transformer secondary is used instead of a delta secondary, particularly at 480 volts or 600 volts. In that case the secondary neutral needs to be taped up. Primary neutral still must be connected to the supply neutral to prevent parasitic overvoltages.
In some cases the secondary system is resistance grounded. Primary neutral still must be connected to the supply neutral. In some cases the secondary grounding electrode system is isolated from the primary neutral.
If you are connecting a wye generator to a wye system using a wye wye transformer then the transformer needs to be a 5 legged or 6 legged core 3-phase unit or three single phase transformers. This is so that any zero sequence voltage or current will magnetize the core(s) so that there will be a zero sequence impedance that will prevent circulating current. A wye generator has almost no zero sequence impedance of its own since zero sequence current produces almost no stator magnetization. The reason why I say almost zero is that a straight phase to neutral single phase load encounters negative and positive sequence impedance which makes things a little more complicated.
If your generator step up transformer is wye-delta-wye then the delta tertiary provides the secondary zero sequence current. Therefore, the generator neutral and tranformer wye winding that is connected to the generator can both be resistor grounded. This gets rid of circulating current in the generator circuit and provides a path for fault current that will operate protective relays for most ground faults in the generator circuit. At the same time, ground fault current is limited to a nondestructive value. However, to detect ground faults close to the neutral point of the generator or transformer primary you need to inject a test current such as 115 volts 400 Hertz from and aircraft ground power unit using a current limiting resistor.