If you intend to book a package will tickets regardless of discounts then definitely book with the tickets. It is very easy to apply a package discount to an existing package but if you have a room only reservation (no tickets) it's a bit more of a pain since the computers can't just switch the type of reservation from room only to package; you have to cancel the room only and rebook as a package.
If you will get the dining plan regardless of discounts then you might as well include it. If there's a chance that you won't want it if the discount doesn't have anything to do with the dining plan then don't include it and add it later. It really doesn't make much difference more than 45 days before your trip but starting at 45 days out it costs extra to make a change that'll result in lowering your vacation cost but the fee is waived if you increase so I personally prefer to include the least I might want and then add as I make up my mind.