Although these settings can be changed at any time, they should first be viewed as part of the system post-installion checks as the site template may have repercussions for things like logo size, adverts etc..
All the templates make allowance for adverts in both the header and side positions. However, if you choose not to use adverts, you may simply choose to recover the additional space the adverts would use on the General Settings of the Adertising Setup page - turn off the adverts to see the setting.All changes you make to this page are applied site-wide immediately you make them. To prevent your users becoming confused, you are advised to only make changes here in times of minimal user interaction on the site.
Note: The changes made here are reflected immediately. As a result, it is almost certain that the home page widgets will have shifted their position. You will need to go to the home page and amend the positions of the widgets to ensure they are aligned correctly.