Perhaps it's because I've started on something that's too advanced for my understanding, but I've reached a point where I'm searching for information that I can't seem to find. I'm attempting to make a fantasy world, races and all, but the map comes first. I've slowly been working on the race histories and such, but that stuff will always feel incomplete without a world for it to take place on. It's basically a metaphorical world in which different races reside. Medieval setting for the story I'm shooting for, and the design is for a fantasy sandbox MMO concept, though I don't think that would help this thread.
To make it simple, I may be shooting for a rather "over-the-top" MMO idea, but I think it's achievable with current tech, or maybe a few years from now. But I'm having trouble with the world itself. The planet is approx. the size of Earth and I'm shooting for a map that I can have everything that I need on one document (kind of like photoshop layers, I can make the climate visible or not, precipitation, where animal/ plant species live, and so on. I've started to make a hand-drawn map but I have to make it small in order for my scanner to get it into illustrator (which I haven't really used at all yet). This causes a detail complication, can't fit much on the size of paper I have at my disposal. A couple issues with the hand-drawing are the mountains, which I can't seem to get right. I'd prefer mountains that portray the area more or less realistically (top-down "topography style" is in mind but I'd also like to do it 3D somehow, I'm just no good at this). And also the rivers, I've looked at many different maps to get how the rivers are supposed to feel, but I can't seem to be satisfied with them, they always seem so "fabricated" even though I think I know where they should go.


So basically, I need help on the following, any assistance would be greatly appreciated:
1.) Is there a program that can hold layers like photoshop, in which I can add details like mountains (topographical or otherwise), rivers maybe, cities, etc. I would prefer the ability to have only one document, simply zoom into the document and add a city on the map (on a new layer), then zoom in to another area and work on a kingdom. If that's asking too much, as I think it is, I won't be devastated, but any programs similar would do fine.
2.) Is there an easy way to put detail onto a map that was hand-drawn and may not be able to accommodate mountains because of the size? If so, which program would I use to do this? (NOTE: I do not have a tablet, only a mouse & keyboard).
3.) How should rivers be on the map? Perhaps, what makes the river's shape? I think I might be missing something in this regard, so any info on it would be appreciated. Or simply, how you think about rivers when making your maps?
4.) I simply don't understand how to unify a map of this size. It'd be easy enough to draw a region and scan it into my comp, but mapping a whole world seems impossible to unify; I can't help but think it would be segmented into "the big map", then the "small maps" with cities on them. I guess this is also number one, but maybe it'll jog different gears in some minds...

Any help is appreciated, I almost feel swamped, but more simply desperate or...reaching the end of the rope in a way. Thanks in advance.