How do I pay it?

Started a new bank account now and wages etc will be paid in there.
Having a bit of trouble working out how it all works.
I get paid X amount a year and the employers pay NI for me.
Then will selling cars and private work I get profits for what I'd call my self employed business which is Y amount a year.
I've got a speadsheet and going to use MS Money as well but that's got what I paid out for parts, fuel and then what I got paid overall so profits.
Is it best to do this personal, or have that as a seperate company then pay myself a set wage? Obviously I know I can't just then use that business account to go buy a PS3!
I want it all above board.
Thank you.
