Structuring an HTML5 Canvas/JS Game

I'm new to HTML5/Canvas/Game programming, but have been tinkering around with it after reading a couple of books. I THINK I have a fairly good idea of how things work out. This question asks several smaller questions, but in general is basically a "structural approach" question. I'm not expecting verbose responses, but hopefully small pointers here and there :) Here is a link to a non-scrolling, and currently rather boring Super Mario World.

Super Mario World Test

NOTE: Controls are Left/Right and Spacebar to jump. This is only setup for Firefox right now as I'm just learning.

Did I Do Something Wrong at This Point?

Currently I've just focused on how Mario runs and jumps, and think that I've gotten it down fairly okay. The coin box doesn't do anything and the background is just an image loaded in for looks. Here's my approach, please let me know if there is anything entirely wrong with this:

Allows Mario to jump by enacting on 2 Y velocities (Gravity and Jump variables)
Allows Mario to run by enacting on 1 velocity (Left or Right "Friction" + Acceleration)
Sprites are used and positioned according to keypress/keydown
I'm not sure if this is right, but I'm using a constructor function to build an object, then inside the main animation loop I'm calling the prototype.draw function for that object to update all variables and redraw the object.
I'm clearing the entire canvas each Frame
Should I be splitting this into more than just a draw function, like Mario.move()?
I've setup a GroundLevel and a JumpLevel variable to create 2 planes of gameplay. The JumpLevel is setup to allow for controlling how high Mario can jump on the fly. The 2 places would allow for the ground to rise like a hill - keeping the point at which Gravity overrules Mario's jumping force at the same distance from the ground.
For clarity sake, everything is separated into different JS files, but would obviously consolidate.

Moving Forward:

Now that I've finished setting up how Mario moves around (I think there are a couple other minor things I might do like mushroom up/down and shooting fireballs). I think I can figure that out, but I'm really lost when it comes to visualizing the following and how HTML5/Canvas can handle this easily:

Scrolling background (I've tried setting up Ground Tiles and using Screen Wrapping, but that seems to cause a lot of uneven issues since I was moving the tiles in the opposite direction. Unfortunately, since I'm trying to account for acceleration, this threw off the count and was causing gaps in the ground. I ditched this idea. Would a DIV beneath the canvas with a large background image be the best solution?
Enemies: Would I create enemies the same way and run a loop for collision detection on every enemy during each frame?
Background Boxes: I'm trying to allow Mario to stand on the boxes in the background, but am unsure how to approach this. I currently have boundaries setup for Mario to stay on the canvas, do I continue to expand these conditions to setup different boundaries based on the boxes? I can see that having several boxes on the screen and doing it this way would get kind of crazy, especially if I would be doing the same hit testing for enemies? I know I'm missing something here....
Level Movement: This is somewhat related. When the Right key is pressed, basically everything in the level needs to move to the left. Would I need to track out all positions of everything that could touch Mario (boxes for him to stand on and enemies for him to collide with) during every animation frame? This seems like it would get kind of inefficient?

Thanks to all! I'll keep this updated with results/solutions :)

Wow, okay. I really like your question because you've obviously done a lot of thinking on this, but partially because of that it's incredibly broad and conversational. You'd do better to find a forum to ask this question.

...That being said, I'm gonna answer the handful of points I'm qualified to, in no particular order. :)

Level Movement: That's a weird (read: inefficient) way to do it. I wouldn't do any calculations based on onscreen positions: track a canonical, camera-agnostic set of coordinates for everything in your level and update the visuals to match. This will stop you from running into weird niggling problems where framerate impacts what you can and can't walk through, or causing slower computers to let Mario run through enemies without being damaged sometimes. Tracking positions this way will incidentally fix a lot of your other problems.
You should absolutely be splitting this into multiple functions. Having movement code and rendering code in the same place is going to screw you, particularly by interacting malignantly with your update/refresh rate. It's going to essentially mean that every time the player does a tricky jump the game does more updates than usual which will make animation/hit detection/etc much less likely to be even.
Enemies: I'd suggest rolling this in with everything else. Do one hit-detection pass against everything, and if you hit something check to see what it was. You could try to optimize this by only checking any given entity against objects within 100 pixels of itself, but if you do it this way you'll need to run separate collision detection events for every enemy. Letting the enemies clip through each other would be computationally cheaper.

Edit: I'd like to clarify about my first point on 'level movement.' Essentially, what you don't want to do is move every entity onscreen every time the camera does, or to store all entity locations as offsets from the camera location (in which case you're still effectively having to move everything, every time the camera moves.)

Your ideal approach is to store your enemy, block, terrain locations with X/Y coordinates that are offset from the absolute top-left of the level (at the very beginning.) In order to render a frame, you'd do essentially this: (pseudocode because we're talking about a hypothetical level format!)

function GetVisible(x,width,level_entities_array) {
  for (i = 0; i < count(level_array); i++){
    if (level_entities_array[i][x] > x && level_entities_array[i][x] < x+width) {
      visible_elements[] = level_entities_array[i][x];
    }
  }
return visible_elements;
}

Boom, you've got everything that should be inside the window. Now you subtract the camera's x offset from the entity's x location and ZAP, you've got its position on the canvas. Pose as a team, 'cause things just got real.

You'll note that I'm not bothering to cull on the Y axis. This can be rectified by extrapolation, which I'm guessing you can handle because you've made it this far. This will be necessary if you want to do any Mario-style vertical exploration.

Yes, I know my pseudocode looks like C# and JavaScript's unholy lovechild. I'm sorry, that's just how I roll at 11:30 at night. ;)