If you want to make changes to layout/position you can do it very quickly or do you change each page manually?
One problem with templating your adsense ads is not being able to specify different channel ids for different pages. This one is a big enough issue for me to not use templates for adsense
I use php for all my sites, then create a file and the only thing in it is the ad code. I pull this in so I only have to edit in one place. <?php include("mainadunit.php"); ?> Code (markup):
I use style sheets, and generally have three or four different types (for contentA, contentB, login, etc.). That way I can just change the style sheet and it'll apply itself across all the relevant pages. I can't do channels for every individual page that way, but I just set up a style sheet for each type of page that I might want a different channel for. Its sort of a hybrid between a single template and doing everything by hand.
I use a content management system that I can make adsense ads as custom blocks. I can specify as many channels as I want and can change site wide settings very quickly.