I did this for one of my sites.
I like to use two different tools simultaneously when trying to figure out what does what files to edit in Magento.
1) I use the web developer toolbar for firefox [every developer should have this installed and use it]
2) I turn on the template path hints in Magento admin panel
a. System > Congiuration
b. Select the Main Website form the scope drop-down
c. Developer > Debug > Template Path Hints = Yes
d. Optional - Add Black Names to Hints = Yes ( I always do this)
e. Save Config
Now, go to your homepage and you will probably freak out. This adds the element names and paths to everything on your page. However, this is exactly what you need to answer your question. See, I just taught you to fish…
So, you checkout where your logo is located and update the template file that specifies the size and location of your logo.
If you are using a custom template, you can go to the skin/frontend route, but if it is something that you want to make permanent, regardless of the skin, I believe that going through the app/ design/frontend route will work just as well.
Good luck, my friend!