Many questions on using blender

I'm new to making mods, so I'm a little clueless on a lot of things (and btw I have watched videos and read that article about making vehicle mods on the wiki). Anyways, here's the current questions i have:
1. If I were to make a panel that crossed over the symmetry line while in symmetry mode, how do i make the two sides into one piece?
2. 3D blocks or flat mesh?
3. How do I attach 2 panels together without making them one?

 

1. When you say 'merge threshold,' do you basically mean they're in the same position in space as each other?
2. I mean should I build the car using the 3D shapes provided like the cube and morph them into the car or should I use the plain instead.
3. Excellent, I'll go look at that later.

Edit: I have another question now about mirror. Whenever I activate it, it reflects on some line that isn't on the middle axis. It seems to be reflecting on a line where this orange dot is (its not part of the design, it was just there on its own accords when I started

 

Great, thanks. But where can I change the merge limit and how do I change where the mirror is?

 

Excellent, thanks for the help. I may have more questions to come
--- Post updated ---
Ok I have another question. If I'm going to build a second body panel on a car, would it be easier to make it by using the first body panel and then cutting away the panel gap or should I just spawn another cube and make it from there?

 

ah, so I could build the whole car out of one shape and then use the boolean operation with some plains to cut each individual panel off

 

Great, thanks again