One Big tilemap or a lot of little tilemap?

#1 Personally I think it would be better to only use one big tilemap per different level. You can always replace whatever tile you want after you get the base tile down (i.e. replacing a grass tile with a dirt tile).

Note: I didn't get much sleep last night so I might be misreading this.

#2 Depends on how big is big. I usually do a tilemap based on the size of the section of the level I'm working on and then I may do another directly on top for layer effects. I also use a doubling so 1024 - 2056 is usually large enough per map then just place them side by side if you need bigger.

That's the best I can do to help without knowing what your designing or why you need to use tilemaps in the first place.