There is a limit online but you can make multiple payments over a series of time for your resort and each of those payments can be with a GC. If you have a room-only reservation, you can pay your balance with GCs when you arrive and you can use as many as it takes to pay it off.
For tickets (including
MNSSHP), you can only use one GC when purchasing online but an unlimited number of them at any ticket booth at the parks.
If you're paying for a dining plan, then I assume that you've got a package. You can pay off your package with GCs by calling Disney reservations or by making multiple payments online as mentioned above. If you've reserved your room through a DVC member and you want to add the dining plan, it would depend on whether you can pay for it with GCs. An individual owner may not want to be bothered with reading off a bunch of GC codes to member services in order to pay for your dining plan. And places like David's don't deal with GCs at all.
You can always open a DVA and deposit the GCs there so that their value is combined (you will earn a $20 Disney GC for every $1000 spent on qualifying purchases). Or you can go to the Disney GC website and combine GCs (up to a total of $1000 on each GC) so that you have fewer GCs to deal with.