Few Noob Questions

[DeadTurtle]

1. How do I shutdown the server properly?
everytime I start the server it displays the message, "InnoDB: Database was not shut down normally!" "InnoDB: Starting Crash Recovery"

I imagine there is somewhere I type something in to signal the server to shutdown which leads me to my next question.

2. Where do I type in server commands? (Ex. Shutdown, Saving server progress, etc...)
Does the progress save automatically, like if my friends and I play all day and gather a bunch of stuff. Then I shut the server down and start it the next day will we still be in the same place?

I am very new to this MySQL stuff so please be patient with me. I am not completely stupid when it comes to this stuff, but I have a lot to learn. Any help and guidance is much appreciated.

 

[DeadTurtle]

Consider this solved. Thank you Faco from the IRC channel.
For others looking for answers to these questions:
To shut down the server properly you will need to install B.E.C. Extended Tools and use the #Shutdown command
(I had a few difficulties getting that going but ultimately I managed to get it.)

Faco said not to worry about saves as save are made periodically.

 

[kitfoo]

That's the one thing I'm trying to figure out...how to restart and shut down the server with a command. Right now, I just literally close the windows, but I know that's not right!