I've done a few long haul flights with just a baby and found the bulkhead seats with bassinet super useful, but have flown just this month with a toddler and a newborn (with no other adults) and while the bassinet was great for the baby it did restrict things with the toddler a bit. On the return journey I didn't get a bulkhead seat and was disappointed but actually there was more space as we had the armrests up for the whole flight. On a long haul this could really work in your favour for the bigger one sleeping.
Some other things to think about:
Would you consider taking a car seat for the toddler? I haven't done this before but have friends who swear by it. If your toddler is used to sleeping in the car seat this could be a winner. It is also better in terms of keeping a toddler in the right place, rather than having them resist seatbelts!! Double and triple check airline requirements and print them off to show any ill-informed check-in staff what you're allowed to bring on the plane. If you take this route I would recommend bulkhead seats.
Emirates is a decent airline so legroom is not too dreadful if you decide to go for the regular seats and hold the baby. (I just flew Turkish Airlines and it was GREAT, I highly recommend it!)
Do you use a baby carrier / sling? If so, definitely take it on the flight as it allows you to be 'hands free' and if the baby is uses to it may be the best way to keep him/her calm and settled. If you're not into them, maybe consider trying one out and seeing if it might work for you for the flights.
Finally - don't worry about asking for help from airline staff and, if necessary, other passengers. I have been very impressed with most staff on Air France, Iberia, and Turkish Airlines, all very helpful and understanding, holding the baby while I went to the loo, helping with bags etc. I have often read horror stories about bad attitudes towards parents/small children on planes and I have certainly witnessed the odd grimace from fellow passengers but I have also been offered help frequently and had people be absolutely lovely. So don't worry about it and if it is difficult and the children are noisy/upset/wet themselves etc, just remind yourself it is only however-many hours and it will be over!!