If you decide against the auto-tipping you are not expected to tip immediately following each act of service to you. The exception here is the room service, where a small gratuity is customary for each trip to your cabin. This is even true for those who stay with the automatic tipping program. I usually give a couple bucks per trip by room service. Obviously if it as unusually large order I would go to $5 or so.
Other than that, you can wait until the end of the cruise and hand out envelopes on the last night of the cruise. However it is also true that for long cruises such as yours, many passengers will tip at the end of each week. Splitting it up like that can be helpful to the crew.
Also - it is perfectly acceptable to not pay the full "suggested amount" for babies. In this case 50% of the suggested amount is fine. Obviously if your cabin attendant or dining room staff does something special for the child you'd want to make note of it. If the child still is in diapers for instance, then the cabin steward will be dealing with disposal of soiled diapers and such.