when you open a docker console the terminal window that opens is just for that docker alone right? So I should be able to update stuff for example apt-get update and upgrade with out it messing with the main unraid os correct?

Correct.

Cool ty, was just double checking before I went nuts in a docker container and didn't want to screw up my unraid setup.

Note that if the docker container is updated on dockerhub then if you use the option to update the docker then you will probably lose any changes made via a terminal session, so make sure you keep track of what you did so you can redo it if necessary.