what happens if you go on a planet that has an atmosphere of "cold/toxic"? Does your character(i'm a thyferran) die? Also, when on the "map" to travel through this one system, there are red blocks around all of the planets, does that mean i'm not allowed to enter without permission or else risk getting attacked?

1/ Currently there are no effects from being on a toxic planet, later on it will affect you if you are not wearing the appropriate protection. Except for a couple of races that don't breathe oxygen.

2/ Hold your mouse over any of the red squares, you'll notice it says "Gravity Well". They're there to signify that that is the range of the gravity well on that planet and thus you can't jump to hyperspace from there.

ah, alright thanks. i'm on a ship assigned to me by my faction, went to try to purchase an NPC, but to put it on the ship i need the ship ID #, how do i figure that out?

You'll need to ask your faction for that or go to Inventory > Ships > Manage Piloted Ships > Show Stats. The ID will be to the right of the name on the left hand side of the page.

How do I leave a planet? I'm on a ship that my faction assigned me to pilot. i'm in the cockpit, and when i click on travel, i have the following options:
Galaxy
Planet
Atmosphere
Descend

Planet > Orbit