1- open the relavant theme.html file.
2- Check and note the name used to display the logo (usually logo.jpg)
3- If a size attribute is included, change these to match your new logo.
4- Rename you new logo to the same name in theme.html
5- Upload logo to your server, overwriting the original logo
6- Go to system admin>preferences>general settings>edit>
7- Make sure theme.html is set to update templates.
8- Click Go.
9- You may need to delete all templates_c content and clear your browser cache to see the changes.

10- in stage 2 above You can or of course change 'logo' to any name you want in theme.html file.

11- What you have done above, will only affect one theme. If you want all your site themes to have the same logo. you will need to repeat this procedure on all theme.html files used and displayed on your site.

12- Note; if templates have already been generated for other themes, you need to make all these themes update as well.

13- In all cases turn your theme update option OFF in admin after new templates have been created and new logo is displayed.