Now, I want to start but.. I don't wanna do things wrong and have to start again so I'd like to clarify some stuff with you guys.[/quote]
Unfortunately, as with anything you will do things wrong and have to start again, this is how we advance as programmers and artists.

My main concern is with drawing the environment. In The Binding of Isaac, was the walls, doors, objects and floor drawn in Illustrator in your opinion or is it Photoshop? Because I've read that I want to work with vectors so it doesn't pixelize when scaled but I don't know if this applies to only the characters or to everything.[/quote]
I don't know what tool the artist used, and in all honesty, it doesn't matter. He could be using vector art, as the lines appear more smooth than raster. If you really want a smooth effect like that, use Flash or Illustrator for making vector art.

When working with Photoshop, what Resolution should I work with when starting a new project?[/quote]
The resolution? Not sure if you mean DPI? DPI only concerns you if you're intending on printing your art. Now if you're asking what pixel size to go with, as in 100x400, this depends on your project.

Should I work with 64x64 pixels tiles? Considering I do work with 64x64 pixels tiles and I want to create the floor tiles, walls and doors for a room type, should I be creating a 640x640 pixels (for example) and apply a 64x64 pixel grid to the view then start drawing. When I'm done, I take out every different tiles and create a tileset from there? What's the good way to work?[/quote]
Your tile size again depends on your project, and what size of tiles your editor will use, or how you prefer to make your map. I personally use sprite sheets, I hate loading tiles by each file. I will load the sheet in my custom World Designer, and cut them in the program.

What is your workflow like when creating characters? Environment?[/quote]
My work flow usually consists of dual monitors. I always keep a 100% preview showing, and I work zoomed in. I also like using tablets.

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With that aside, everything for making games will come with experience, so keep trying new things. All of the countless times I messed up on projects in turn left me learning more by researching, and trying new ideas. It's been over 10 years, and I've learned a lot from my mistakes!

I keep my Resolution at 72, or 300 for concept art.

One needs to understand how he made the game. For example, he could be using 32x32 tiles, and have an object sprite for the door which is placed over top. My World Designer consists of three layers: Tiles / Objects / Sprites(Enemies/Players). There are several ways to go about doing what he did.

I use 40x40 tiles in my game because my map sizes are 1600 x 1200, and to tile evenly you need to be able to divide 40 by the width and height, which means 40 tiles wide, 30 tiles long.

All you do with tiling is make each individual tile. Wall - Top / Wall - Right / Wall - Top Right, ect... Then you either use a Map Editor, or program one that allows you to map levels out, or just us a 2D Array / Vector to make a map. Then draw it to the screen with your Graphics API.

I create a character by sketching a basic model, and just adding layers from there. It's a lot more complex than that though as it takes different approaches to find a way that works best with your style.

This one for example was just random scribbling to get a concept. Once I find something that might work, I take it to the next step.

Learn about scrollable maps! I might only have a certain amount of the map visible due to the camera, so I use a tile size that works for my map sizes. Don't believe you're locked into any "format" for making a map or even your game for that matter.

Like I said before, your tile size is based on how you're programming your game, and how the levels are built.