You are automatically level 2 when you hit 1000... or is it 1001? Probably 1000. You should have gotten a message about your new HP. Your skill point will be available in your pool under Manage -> Character. If you want to spend it now go ahead, although a lot of people would recommend holding on to them until more features are complete.
"May the Grace of Ara go with you, and His Vengeance be wrought upon your enemies."