1) What's the source of the zombies? Can you really find that many dead folks?
Yes, you can really find that many dead people. My town/city has an surface of 5.5 x 5.5 km (~3 x ~3 miles) and 100.000 inhabitants. At the infamous turning point (50% is zombies) there would be 50.000 zombies on 9 square miles or about 5.000 zombies/sqr mile. The problem then is that zombies are drawn to people. Zombies will leave the bedrooms, storagerooms or fitting rooms and go to places were survivors go. That way the only mall on a sqr mile might have 2.500 zombies outside. That's a lot. There is a reason people always want to go to the countryside, a lot less people, so a lot less potential zombies.
2) What are the resources the PCs have? Can you stretch those out somehow?
There are two possible situations, zombies in the USA(or another country with legal weapons) or zombies in a country were weapons aren't legal.
USA:
Zombies don't use guns. This means that when the percentage of zombies rises, the number of guns per potential user rises. If you watch a classic zombie movie set in the USA, you'll see that ammo is the biggest concern. Guns are quite disposable, but you need to be careful with ammo. Converting this into a game, the 'USA'-type zombie game will be more of a resource-management game. "If we shoot ourselves trough this encounter, we'll have 20 bullets left each. That means that the mall can have a max of N zombies, or otherwise we'll have to visit a gunstore first.". I you go with this, I would also include med-kits, and maybe a food and water system. to make the resources somewhat more diverse.
Not-USA:
Watching 28 Days later, you'll see that they don't have any weapon. The most heavily armed 'normal' survivor has a riot-police kit. These movies mostly are about sneaking past as much zombies as possible and getting to a 'safe spot', mostly an army outpost or something similar.
3) Where are the PCs?
Probably in a city, because there be zombies. They will probably want to go the the countryside, but first need guns (in USA-type), canned food and water, get means of transport and then get out of town.
4) Do the PCs need to just hole up and fend off hordes, or can you force them to sneak out and save survivors?
In most stories the survivors are not happy with a hiding place in the city, and have to follow the step-by-step plan as set in (3). Rescuing survivors is mostly not a priority, unless it's someone related to the PC's. You'll see that Good isn't a wise alignment when encountering zombies. You could ofcourse let survivors be a resource, especially if your game isn't RP-centered, player could respawn if they have an survivor handy.
5) What are the overall effects on the Setting? Longterm?
Nasty. If the player manage to find an suitable hiding place that they don't or rarely have to leave, than you'll have to think about the lifespan of zombies. Do they die in a month? A year? Never? I think there are three stages:
-Getting safe
-Staying safe
-Rebuilding the world
6) What kind of zombies are these?
Lot's. 28 days later has a 'rage' virus, that makes people somewhat angry. It also could be a organism that kill people and than uses it's muscles and stuff to create a way of transmitting itself. Voodoo has magical zombies.
I hope this is all clear and helpful to you, and otherwise, ask away, I'll stick around
Nummlock