That depends...most free counters make you display a graphic that shows were the counter is based. We're using Bravenet for the site here. They allow you to have 3 different counters. So we added one in the inc_footer.asp that is visible for the non-forum pages. (like you see here: http://forum.snitz.com/) For that one to display correctly we added it in the same row as the Powered By logo (just take a look at the source of that page). We alse added 2 more counters in the inc_footer.asp of the forum pages. The nice thing about those is that you don't see them unless you look in the source. Bravenet allows you to set the image size to 0. In this case it doesn't really matter were you put them in the footer (you can see ours by looking at the source of any forum page).
Why dit we use 2 counters for the forum ? Well we've set one to count visits and the other to count hits ! We could/should of course add the hitcounter to the popup page footer also to have it count correctly but this gives a accurate enough impression of the huge number of hits we get.