Log into your ACP, and go to Styles & Templates, then choose the skin you want to put them in, and determine where you want them. I put mine in the FORUMDISPLAY and SHOWTHREAD templates, as well as FOOTER template. If you use the first two, put the code below the navbar and header.
Let me know if you need any help.
If I use the footer option, where would be the best place to put the ad code?